@article {pmid35041771, year = {2022}, author = {Ahearn-Ford, S and Berrington, JE and Stewart, CJ}, title = {Development of the gut microbiome in early life.}, journal = {Experimental physiology}, volume = {}, number = {}, pages = {}, doi = {10.1113/EP089919}, pmid = {35041771}, issn = {1469-445X}, abstract = {NEW FINDINGS: What is the topic of this review? This symposium report discusses the importance of the early life gut microbiome, with a focus on preterm infants and microbially-related diseases. Current techniques to study the preterm gut microbiome are appraised, and the potential of recent methodological advancements is discussed. What advances does it highlight? Recent findings in the field achieved by the application of advanced technologies are acknowledged. The review also highlights the applicability of intestinal-derived organoid models to study host-microbiome interactions in the preterm gut, and recent developments in enhancing the physiological relevance of such models. Preterm intestinal-derived organoids may provide novel insights into the mechanisms underlying preterm disease, as well as diagnosis and treatment opportunities. These models have huge translational potential, offering a step towards precision medicine.<br><br>ABSTRACT: Accumulating evidence affirms the importance of the gut microbiome in both health and disease. In early life, there exists a critical period in which the composition of gut microbes is particularly malleable and subject to a wide range of influencing factors. Disturbances to microbial communities during this time may be beneficial or detrimental to short and long-term health outcomes. For infants born prematurely, naïve immune systems, immature gastrointestinal tracts and additional clinical needs put this population at high risk of abnormal microbial colonisation, resulting in an increased susceptibility to diseases including necrotising enterocolitis (NEC) and late-onset sepsis (LOS). Traditional cell culture methods, gnotobiotic animals, molecular sequencing techniques (16S rRNA gene sequencing and metagenomics) and advanced "omics" technologies (transcriptomics, proteomics and metabolomics) have been fundamental in exploring the associations between diet, gut microbes, microbial functions, and disease. Despite significant investment and ongoing research efforts, prevention and treatment strategies in NEC and LOS remain limited. Recent endeavours have focused on searching for new, more physiologically relevant models to simulate the preterm intestine. Preterm intestinal-derived organoids represent a promising in vitro approach in the study of host-microbial interactions in the preterm infant gut, offering new and exciting possibilities in this field. This article is protected by copyright. All rights reserved.}, }
@article {pmid35040752, year = {2022}, author = {Chen, Y and Wang, H and Lu, W and Wu, T and Yuan, W and Zhu, J and Lee, YK and Zhao, J and Zhang, H and Chen, W}, title = {Human gut microbiome aging clocks based on taxonomic and functional signatures through multi-view learning.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2025016}, doi = {10.1080/19490976.2021.2025016}, pmid = {35040752}, issn = {1949-0984}, abstract = {The human gut microbiome is a complex ecosystem that is closely related to the aging process. However, there is currently no reliable method to make full use of the metagenomics data of the gut microbiome to determine the age of the host. In this study, we considered the influence of geographical factors on the gut microbiome, and a total of 2604 filtered metagenomics data from the gut microbiome were used to construct an age prediction model. Then, we developed an ensemble model with multiple heterogeneous algorithms and combined species and pathway profiles for multi-view learning. By integrating gut microbiome metagenomics data and adjusting host confounding factors, the model showed high accuracy (R2 = 0.599, mean absolute error = 8.33 years). Besides, we further interpreted the model and identify potential biomarkers for the aging process. Among these identified biomarkers, we found that Finegoldia magna, Bifidobacterium dentium, and Clostridium clostridioforme had increased abundance in the elderly. Moreover, the utilization of amino acids by the gut microbiome undergoes substantial changes with increasing age which have been reported as the risk factors for age-associated malnutrition and inflammation. This model will be helpful for the comprehensive utilization of multiple omics data, and will allow greater understanding of the interaction between microorganisms and age to realize the targeted intervention of aging.}, }
@article {pmid35040702, year = {2022}, author = {Dragone, NB and Henley, JB and Holland-Moritz, H and Diaz, M and Hogg, ID and Lyons, WB and Wall, DH and Adams, BJ and Fierer, N}, title = {Elevational Constraints on the Composition and Genomic Attributes of Microbial Communities in Antarctic Soils.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0133021}, doi = {10.1128/msystems.01330-21}, pmid = {35040702}, issn = {2379-5077}, abstract = {The inland soils found on the Antarctic continent represent one of the more challenging environments for microbial life on Earth. Nevertheless, Antarctic soils harbor unique bacterial and archaeal (prokaryotic) communities able to cope with extremely cold and dry conditions. These communities are not homogeneous, and the taxonomic composition and functional capabilities (genomic attributes) of these communities across environmental gradients remain largely undetermined. We analyzed the prokaryotic communities in soil samples collected from across the Shackleton Glacier region of Antarctica by coupling quantitative PCR, marker gene amplicon sequencing, and shotgun metagenomic sequencing. We found that elevation was the dominant factor explaining differences in the structures of the soil prokaryotic communities, with the drier and saltier soils found at higher elevations harboring less diverse communities and unique assemblages of cooccurring taxa. The higher-elevation soil communities also had lower maximum potential growth rates (as inferred from metagenome-based estimates of codon usage bias) and an overrepresentation of genes associated with trace gas metabolism. Together, these results highlight the utility of assessing community shifts across pronounced environmental gradients to improve our understanding of the microbial diversity found in Antarctic soils and the strategies used by soil microbes to persist at the limits of habitability. IMPORTANCE Antarctic soils represent an ideal system to study how environmental properties shape the taxonomic and functional diversity of microbial communities given the relatively low diversity of Antarctic soil microbial communities and the pronounced environmental gradients that occur across soils located in reasonable proximity to one another. Moreover, the challenging environmental conditions typical of most Antarctic soils present an opportunity to investigate the traits that allow soil microbes to persist in some of the most inhospitable habitats on Earth. We used cultivation-independent methods to study the bacterial and archaeal communities found in soil samples collected from across the Shackleton Glacier region of the Transantarctic Mountains. We show that those environmental characteristics associated with elevation have the greatest impact on the structure of these microbial communities, with the colder, drier, and saltier soils found at higher elevations sustaining less diverse communities that were distinct from those in more hospitable soils with respect to their composition, genomic attributes, and overall life-history strategies. Notably, the harsher conditions found in higher-elevation soils likely select for taxa with lower maximum potential growth rates and an increased reliance on trace gas metabolism to support growth.}, }
@article {pmid35039619, year = {2022}, author = {Mousavi, SH and Sadeghian Motahar, SF and Salami, M and Kavousi, K and Sheykh Abdollahzadeh Mamaghani, A and Ariaeenejad, S and Salekdeh, GH}, title = {Author Correction: In vitro bioprocessing of corn as poultry feed additive by the influence of carbohydrate hydrolyzing metagenome derived enzyme cocktail.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1176}, doi = {10.1038/s41598-022-05555-7}, pmid = {35039619}, issn = {2045-2322}, }
@article {pmid35039616, year = {2022}, author = {Zheng, X and Jahn, MT and Sun, M and Friman, VP and Balcazar, JL and Wang, J and Shi, Y and Gong, X and Hu, F and Zhu, YG}, title = {Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {35039616}, issn = {1751-7370}, support = {RSG\R1\180213//Royal Society/ ; }, abstract = {Viruses significantly influence local and global biogeochemical cycles and help bacteria to survive in different environments by encoding various auxiliary metabolic genes (AMGs) associated with energy acquisition, stress tolerance and degradation of xenobiotics. Here we studied whether bacterial (dsDNA) virus encoded AMGs are enriched in organochlorine pesticide (OCP) contaminated soil in China and if viral AMGs include genes linked to OCP biodegradation. Using metagenomics, we found that OCP-contaminated soils displayed a lower bacterial, but higher diversity of viruses that harbored a higher relative abundance of AMGs linked to pesticide degradation and metabolism. Furthermore, the diversity and relative abundance of AMGs significantly increased along with the severity of pesticide contamination, and several biodegradation genes were identified bioinformatically in viral metagenomes. Functional assays were conducted to experimentally demonstrate that virus-encoded L-2-haloacid dehalogenase gene (L-DEX) is responsible for the degradation of L-2-haloacid pesticide precursors, improving bacterial growth at sub-inhibitory pesticide concentrations. Taken together, these results demonstrate that virus-encoded AMGs are linked to bacterial metabolism and biodegradation, being more abundant and diverse in soils contaminated with pesticides. Moreover, our findings highlight the importance of virus-encoded accessory genes for bacterial ecology in stressful environments, providing a novel avenue for using viruses in the bioremediation of contaminated soils.}, }
@article {pmid35039534, year = {2022}, author = {Lee, SJ and Rho, M}, title = {Multimodal deep learning applied to classify healthy and disease states of human microbiome.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {824}, pmid = {35039534}, issn = {2045-2322}, support = {2017M3A9F3041232//National Research Foundation of Korea/ ; 2020-0-01373//Institute of Information &amp; Communications Technology Planning &amp; Evaluation (IITP)/ ; }, abstract = {Metagenomic sequencing methods provide considerable genomic information regarding human microbiomes, enabling us to discover and understand microbial diseases. Compositional differences have been reported between patients and healthy people, which could be used in the diagnosis of patients. Despite significant progress in this regard, the accuracy of these tools needs to be improved for applications in diagnostics and therapeutics. MDL4Microbiome, the method developed herein, demonstrated high accuracy in predicting disease status by using various features from metagenome sequences and a multimodal deep learning model. We propose combining three different features, i.e., conventional taxonomic profiles, genome-level relative abundance, and metabolic functional characteristics, to enhance classification accuracy. This deep learning model enabled the construction of a classifier that combines these various modalities encoded in the human microbiome. We achieved accuracies of 0.98, 0.76, 0.84, and 0.97 for predicting patients with inflammatory bowel disease, type 2 diabetes, liver cirrhosis, and colorectal cancer, respectively; these are comparable or higher than classical machine learning methods. A deeper analysis was also performed on the resulting sets of selected features to understand the contribution of their different characteristics. MDL4Microbiome is a classifier with higher or comparable accuracy compared with other machine learning methods, which offers perspectives on feature generation with metagenome sequences in deep learning models and their advantages in the classification of host disease status.}, }
@article {pmid35039079, year = {2022}, author = {Adu-Oppong, B and Thänert, R and Wallace, MA and Burnham, CD and Dantas, G}, title = {Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {6}, pmid = {35039079}, issn = {2049-2618}, abstract = {BACKGROUND: The lack of a definition of urinary microbiome health convolutes diagnosis of urinary tract infections (UTIs), especially when non-traditional uropathogens or paucity of bacteria are recovered from symptomatic patients in routine standard-of-care urine tests. Here, we used shotgun metagenomic sequencing to characterize the microbial composition of asymptomatic volunteers in a set of 30 longitudinally collected urine specimens. Using permutation tests, we established a range of asymptomatic microbiota states, and use these to contextualize the microbiota of 122 urine specimens collected from patients with suspected UTIs diagnostically categorized by standard-of-care urinalysis within that range. Finally, we used a standard-of-care culture protocol to evaluate the efficiency of culture-based recovery of the urinary microbiota.<br><br>RESULTS: The majority of genitourinary microbiota in individals suspected to have UTI overlapped with the spectrum of asymptomatic microbiota states. Longitudinal characterization of the genitourinary microbiome in urine specimens collected from asymptomatic volunteers revealed fluctuations of microbial functions and taxonomy over time. White blood cell counts from urinalysis suggested that urine specimens categorized as 'insignificant', 'contaminated', or 'no-growth' by conventional culture methods frequently showed signs of urinary tract inflammation, but this inflammation is not associated with genitourinary microbiota dysbiosis. Comparison of directly sequenced urine specimens with standard-of-care culturing confirmed that culture-based diagnosis biases genitourinary microbiota recovery towards the traditional uropathogens Escherichia coli and Klebsiella pneumoniae.<br><br>CONCLUSION: Here, we utilize shotgun metagenomic sequencing to establish a baseline of asymptomatic genitourinary microbiota states. Using this baseline we establish substantial overlap between symptomatic and asymptomatic genitourinary microbiota states. Our results establish that bacterial presence alone does not explain the onset of clinical symptoms. Video Abstract.}, }
@article {pmid35038864, year = {2022}, author = {Xie, J and Jin, L and Wu, D and Pruden, A and Li, X}, title = {Inhalable Antibiotic Resistome from Wastewater Treatment Plants to Urban Areas: Bacterial Hosts, Dissemination Risks, and Source Contributions.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.1c07023}, pmid = {35038864}, issn = {1520-5851}, abstract = {Antibiotic resistance genes (ARGs) are commonly detected in the atmosphere, but questions remain regarding their sources and relative contributions, bacterial hosts, and corresponding human health risks. Here, we conducted a qPCR- and metagenomics-based investigation of inhalable fine particulate matter (PM2.5) at a large wastewater treatment plant (WWTP) and in the ambient air of Hong Kong, together with an in-depth analysis of published data of other potential sources in the area. PM2.5 was observed with increasing enrichment of total ARGs along the coastal-urban-WWTP gradient and clinically relevant ARGs commonly identified in urban and WWTP sites, illustrating anthropogenic impacts on the atmospheric accumulation of ARGs. With certain kinds of putative antibiotic-resistant pathogens detected in urban and WWTP PM2.5, a comparable proportion of ARGs that co-occurred with MGEs was found between the atmosphere and WWTP matrices. Despite similar emission rates of bacteria and ARGs within each WWTP matrix, about 11-13% of the bacteria and >57% of the relevant ARGs in urban and WWTP PM2.5 were attributable to WWTPs. Our study highlights the importance of WWTPs in disseminating bacteria and ARGs to the ambient air from a quantitative perspective and, thus, the need to control potential sources of inhalation exposure to protect the health of urban populations.}, }
@article {pmid35038509, year = {2022}, author = {Wen, L and Huang, L and Wang, Y and Yuan, Y and Zhou, L}, title = {Facet-engineered hematite boosts microbial electrogenesis by synergy of promoting electroactive biofilm formation and extracellular electron transfer.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {153154}, doi = {10.1016/j.scitotenv.2022.153154}, pmid = {35038509}, issn = {1879-1026}, abstract = {Hematite has been proven to be an excellent material for enhancing extracellular electron transfer (EET) in microbial bioelectrochemical systems (BESs). However, the effect of hematite with different exposed facets on microbial EET remains unclear. Here, we synthesized two types of hematite nanoparticles with high {100} and {001} facet exposure (Hem_{100} and Hem_{001}), respectively, which were coated on ITO electrode to stimulate the microbial EET in the BESs. The results showed that the maximum biocurrent density of commercial hematite nanoparticles (Hem_NPs), Hem_{100} and Hem_{001} electrodes reached 73.33 ± 5.68, 129.33 ± 9.12 and 287.00 ± 19.89 μA cm-2 from three replicates of each treatment, respectively. The current generation achieved from the Hem_{001} electrode was nearly 199-times higher than that of the blank ITO electrode (1.44 ± 0.10 μA cm-2). The electrochemical measurements showed that the lowest charge transfer resistance (Rct) was observed for the Hem_{001}, and the promoted biofilm formation and EPS secretion on the Hem_{001} electrode were also revealed, which could contribute the high performance of this electrode. Moreover, metagenomic analysis revealed that Hem_{001} might facilitate the microbial EET by stimulating the expression of genes related to cytochrome c and conductive nanowires. This study not only provides a new strategy to enhance microbial electrogenesis but also expands the knowledge of the effect of facet on microbial EET, helping to develop more efficient electrode materials in the future.}, }
@article {pmid35038012, year = {2022}, author = {Zhou, SP and Zhou, HY and Sun, JC and Liu, C and Ke, X and Zou, SP and Xue, YP and Zheng, YG}, title = {Bacterial dynamics and functions driven by bulking agents to enhance organic degradation in food waste in-situ rapid biological reduction (IRBR).}, journal = {Bioprocess and biosystems engineering}, volume = {}, number = {}, pages = {}, pmid = {35038012}, issn = {1615-7605}, abstract = {This study investigated the effects of different bulking agents (i.e., sawdust, wheat straw, rice straw, and corncob) on bacterial structure and functions for organic degradation during food waste in-situ rapid biological reduction (IRBR) inoculated with microbial agent. Results showed that the highest organic degradation (409.5 g/kg total solid) and volatile solids removal efficiency (41.0%) were achieved when wheat straw was used, largely because the degradation of readily degradable substrates and cellulose was promoted by this bulking agent. Compared with other three bulking agents, the utilization of wheat straw was conducive to construct a more suitable environmental condition (moisture content of 18.0-28.2%, pH of 4.91-5.87) for organic degradation during IRBR process, by virtue of its excellent structural and physiochemical properties. Microbial community analysis suggested that the high-moisture environment in rice straw treatment promoted the growth of Staphylococcus and inhibited the activity of the inoculum. By contrast, lowest bacterial richness was observed in corncob treatment due to the faster water loss. Compared with these two bulking agents, sawdust and wheat straw treatment led to a more stable bacterial community structure, and the inoculated Bacillus gradually became the dominant genus (36.6-57.8%) in wheat straw treatment. Predicted metagenomics analysis showed that wheat straw treatment exhibited the highest carbohydrate metabolism activity which improved the pyruvate, amino sugar and nucleotide sugar metabolism, and thereby promoted the organic degradation and humic substrate production. These results indicated that wheat straw was a more desirable bulking agent, and revealed the potential microbial organics degradation mechanism in IRBR process.}, }
@article {pmid35037933, year = {2022}, author = {Costa, SS and Lago, LAB and Silva, A and Graças, DAD and Lameira, J and Baraúna, RA}, title = {Diversity of bacteriocins in the microbiome of the Tucuruí Hydroelectric Power Plant water reservoir and three-dimensional structure prediction of a zoocin.}, journal = {Genetics and molecular biology}, volume = {45}, number = {1}, pages = {e20210204}, doi = {10.1590/1678-4685-GMB-2021-0204}, pmid = {35037933}, issn = {1415-4757}, abstract = {Bacteriocins are antimicrobial peptides expressed by bacteria through ribosomal activity. In this study, we analyzed the diversity of bacteriocin-like genes in the Tucuruí-HPP using a whole-metagenome shotgun sequencing approach. Three layers of the water column were analyzed (photic, aphotic and sediment). Detection of bacteriocin-like genes was performed with blastx using the BAGEL4 database as subject sequences. In order to calculate the abundance of bacteriocin-like genes we also determined the number of 16S rRNA genes using blastn. Taxonomic analysis was performed using RAST server and the metagenome was assembled using IDBA-UD in order to recover the full sequence of a zoocin which had its three-dimensional structure determined. The photic zone presented the highest number of reads affiliated to bacteriocins. The most abundant bacteriocins were sonorensin, Klebicin D , pyocin and colicin. The zoocin model was composed of eight anti-parallel β-sheets and two α-helices with a Zn2+ ion in the active site. This model was considerably stable during 10 ns of molecular dynamics simulation. We observed a high diversity of bacteriocins in the Tucuruí-HPP, demonstrating that the environment is an inexhaustible source for prospecting these molecules. Finally, the zoocin model can be used for further studies of substrate binding and molecular mechanisms involving peptidoglycan degradation.}, }
@article {pmid35037767, year = {2022}, author = {Shen, Y and Laue, HE and Shrubsole, MJ and Wu, H and Bloomquist, TR and Larouche, A and Zhao, K and Gao, F and Boivin, A and Prada, D and Hunting, DJ and Gillet, V and Takser, L and Baccarelli, AA}, title = {Associations of Childhood and Perinatal Blood Metals with Children's Gut Microbiomes in a Canadian Gestation Cohort.}, journal = {Environmental health perspectives}, volume = {130}, number = {1}, pages = {17007}, doi = {10.1289/EHP9674}, pmid = {35037767}, issn = {1552-9924}, abstract = {BACKGROUND: The gut microbiome is important in modulating health in childhood. Metal exposures affect multiple health outcomes, but their ability to modify bacterial communities in children is poorly understood.<br><br>OBJECTIVES: We assessed the associations of childhood and perinatal blood metal levels with childhood gut microbiome diversity, structure, species, gene family-inferred species, and potential pathway alterations.<br><br>METHODS: We assessed the gut microbiome using 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing in stools collected from 6- to 7-year-old children participating in the GESTation and Environment (GESTE) cohort study. We assessed blood metal concentrations [cadmium (Cd), manganese (Mn), mercury (Hg), lead (Pb), selenium (Se)] at two time points, namely, perinatal exposures at delivery (N=70) and childhood exposures at the 6- to 7-y follow-up (N=68). We used multiple covariate-adjusted statistical models to determine microbiome associations with continuous blood metal levels, including linear regression (Shannon and Pielou alpha diversity indexes), permutational multivariate analysis of variance (adonis; beta diversity distance matrices), and multivariable association model (MaAsLin2; phylum, family, species, gene family-inferred species, and pathways).<br><br>RESULTS: Children's blood Mn and Se significantly associated with microbiome phylum [e.g., Verrucomicrobiota (coef=-0.305, q=0.031; coef=0.262, q=0.084, respectively)] and children's blood Mn significantly associated with family [e.g., Eggerthellaceae (coef=-0.228, q=0.052)]-level differences. Higher relative abundance of potential pathogens (e.g., Flavonifractor plautii), beneficial species (e.g., Bifidobacterium longum, Faecalibacterium prausnitzii), and both potentially pathogenic and beneficial species (e.g., Bacteriodes vulgatus, Eubacterium rectale) inferred from gene families were associated with higher childhood or perinatal blood Cd, Hg, and Pb (q<0.1). We found significant negative associations between childhood blood Pb and acetylene degradation pathway abundance (q<0.1). Finally, neither perinatal nor childhood metal concentrations were associated with children's gut microbial inter- and intrasubject diversity.<br><br>DISCUSSION: Our findings suggest both long- and short-term associations between metal exposure and the childhood gut microbiome, with stronger associations observed with more recent exposure. Future epidemiologic analyses may elucidate whether the observed changes in the microbiome relate to children's health. https://doi.org/10.1289/EHP9674.}, }
@article {pmid35037474, year = {2022}, author = {Rayo, E and Ferrari, G and Neukamm, J and Akgül, G and Breidenstein, AM and Cooke, M and Phillips, C and Bouwman, AS and Rühli, FJ and Schuenemann, VJ}, title = {Non-destructive extraction of DNA from preserved tissues in medical collections.}, journal = {BioTechniques}, volume = {}, number = {}, pages = {}, doi = {10.2144/btn-2021-0014}, pmid = {35037474}, issn = {1940-9818}, support = {URPP Evolution in Action pilot project grant//Universität Zürich/ ; }, abstract = {Museum specimens and histologically fixed material are valuable samples for the study of historical soft tissues and represent a possible pathogen-specific source for retrospective molecular investigations. However, current methods for molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology, thus damaging the sample, and conserving the material for future investigations. Here the authors present the first tests of a non-destructive alternative that facilitates genetic analysis of fixed wet tissues while avoiding tissue damage. The authors extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. The results show that human historical DNA can be retrieved from the fixative material of medical specimens and provide new options for sampling valuable collections.}, }
@article {pmid35036827, year = {2021}, author = {Goller, CC and Srougi, MC and Chen, SH and Schenkman, LR and Kelly, RM}, title = {Integrating Bioinformatics Tools Into Inquiry-Based Molecular Biology Laboratory Education Modules.}, journal = {Frontiers in education}, volume = {6}, number = {}, pages = {}, doi = {10.3389/feduc.2021.711403}, pmid = {35036827}, issn = {2504-284X}, abstract = {The accelerating expansion of online bioinformatics tools has profoundly impacted molecular biology, with such tools becoming integral to the modern life sciences. As a result, molecular biology laboratory education must train students to leverage bioinformatics in meaningful ways to be prepared for a spectrum of careers. Institutions of higher learning can benefit from a flexible and dynamic instructional paradigm that blends up-to-date bioinformatics training with best practices in molecular biology laboratory pedagogy. At North Carolina State University, the campus-wide interdisciplinary Biotechnology (BIT) Program has developed cutting-edge, flexible, inquiry-based Molecular Biology Laboratory Education Modules (MBLEMs). MBLEMs incorporate relevant online bioinformatics tools using evidenced-based pedagogical practices and in alignment with national learning frameworks. Students in MBLEMs engage in the most recent experimental developments in modern biology (e.g., CRISPR, metagenomics) through the strategic use of bioinformatics, in combination with wet-lab experiments, to address research questions. MBLEMs are flexible educational units that provide a menu of inquiry-based laboratory exercises that can be used as complete courses or as parts of existing courses. As such, MBLEMs are designed to serve as resources for institutions ranging from community colleges to research-intensive universities, involving a diverse range of learners. Herein, we describe this new paradigm for biology laboratory education that embraces bioinformatics as a critical component of inquiry-based learning for undergraduate and graduate students representing the life sciences, the physical sciences, and engineering.}, }
@article {pmid35036659, year = {2021}, author = {Borroni, D and Rachwani-Anil, R and González, JMS and Rodríguez-Calvo-de-Mora, M and Rocha de Lossada, C}, title = {Metagenome techniques to reduce diagnostic delay in Acanthamoeba keratitis.}, journal = {Romanian journal of ophthalmology}, volume = {65}, number = {3}, pages = {307-308}, doi = {10.22336/rjo.2021.63}, pmid = {35036659}, issn = {2501-2533}, }
@article {pmid35036494, year = {2022}, author = {Tran, DM and Huynh, TU and Nguyen, TH and Do, TO and Tran, TPH and Nguyen, QV and Nguyen, AD}, title = {Soil microbiome dataset from Yok Don national park in the Central Highlands region of Vietnam.}, journal = {Data in brief}, volume = {40}, number = {}, pages = {107798}, doi = {10.1016/j.dib.2022.107798}, pmid = {35036494}, issn = {2352-3409}, abstract = {The Central Highlands region contains most of the national parks in Vietnam with different ecosystems, including the national parks of Kon Ka Kinh, Chu Mon Ray, Chu Yang Sin, Yok Don, Bidoup-Nui Ba, and Ta Dung. Thus, this region is considered a center with the highest biodiversity in Vietnam [1]. Among the national parks, Yok Don is unique in its conservation of the dry deciduous dipterocarp forest. Furthermore, Yok Don is the second-largest park in Vietnam; it has the most different ecosystem compared with other national parks in this region [2]. Although some studies have investigated biodiversity preservation in the region, some other studies have only dealt with medicinal plants, lichens, and the rhizospheric bacteria of cultivated black pepper [1,[3], [4], [5]. To the best of our knowledge, no research on the microbial communities in Yok Don national park and in the Central Highlands has been reported. At present, global warming and a decrease in the forest area in the Central Highlands have led to the ongoing reduction in biodiversity and microbial resources. The current study reports the microbiome dataset from the soil sample collected in Yok Don national park. Metagenomic next-generation sequencing was used to characterize the microbial communities in the sample. The metagenome dataset generated provides information on microbial diversity and its functionality and can be useful for further studies on the conservation and use of microbial genetic resources in this region.}, }
@article {pmid35035791, year = {2022}, author = {Piquer-Esteban, S and Ruiz-Ruiz, S and Arnau, V and Diaz, W and Moya, A}, title = {Exploring the universal healthy human gut microbiota around the World.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {421-433}, pmid = {35035791}, issn = {2001-0370}, abstract = {The human gut holds a special place in the study of different microbial environments due to growing evidence that the gut microbiota is related to host health. However, despite extensive research, there is still a lack of knowledge about the core taxa forming the gut microbiota and, moreover, available information is biased towards western microbiomes in both genome databases and most core taxa studies. To tackle these limitations, we tested a database enrichment strategy and analyzed public datasets of whole-genome shotgun data, generated from 545 fecal samples, comprising three gradients of westernization. The NT database was selected as a baseline of biological diversity, subsequently being combined with various studies of interest related to the human microbiota. This enrichment strategy made it possible to improve classification capacity, compared to the original unenriched database, regarding the various lifestyles and populations studied. The effects of incomplete-taxonomy metagenome-assembled genomes on genome database enrichment were also examined, revealing that, while they are helpful, they should be used with caution depending on the taxonomic level of interest. Moreover, in terms of high prevalence, the core analysis revealed a conserved set of bacterial taxa in the healthy human gut microbiota worldwide, despite apparent lifestyle differences. Such taxa show a set of traits, metabolic roles, and ancestral status, making them suitable candidates for a hypothetical phylogenetic core of mutualistic microorganisms co-evolving with the human species.}, }
@article {pmid35035382, year = {2021}, author = {Díaz-García, L and Chaparro, D and Jiménez, H and Gómez-Ramírez, LF and Bernal, AJ and Burbano-Erazo, E and Jiménez, DJ}, title = {Top-Down Enrichment Strategy to Co-cultivate Lactic Acid and Lignocellulolytic Bacteria From the Megathyrsus maximus Phyllosphere.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {744075}, pmid = {35035382}, issn = {1664-302X}, abstract = {Traditionally, starting inoculants have been applied to improve ensiling of forage used for livestock feed. Here, we aimed to build up a bioinoculant composed of lactic acid-producing and lignocellulolytic bacteria (LB) derived from the Megathyrsus maximus (guinea grass) phyllosphere. For this, the dilution-to-stimulation approach was used, including a sequential modification of the starting culture medium [Man, Rogosa, and Sharpe (MRS) broth] by addition of plant biomass (PB) and elimination of labile carbon sources. Along 10 growth-dilution steps (T1-T10), slight differences were observed in terms of bacterial diversity and composition. After the sixth subculture, the consortium started to degrade PB, decreasing its growth rate. The co-existence of Enterobacteriales (fast growers and highly abundance), Actinomycetales, Bacillales, and Lactobacillales species was observed at the end of the selection process. However, a significant structural change was noticed when the mixed consortium was cultivated in higher volume (500ml) for 8days, mainly increasing the proportion of Paenibacillaceae populations. Interestingly, Actinomycetales, Bacillales, and Lactobacillales respond positively to a pH decrease (4-5), suggesting a relevant role within a further silage process. Moreover, gene-centric metagenomic analysis showed an increase of (hemi)cellulose-degrading enzymes (HDEs) during the enrichment strategy. Reconstruction of metagenome-assembled genomes (MAGs) revealed that Paenibacillus, Cellulosimicrobium, and Sphingomonas appear as key (hemi)cellulolytic members (harboring endo-glucanases/xylanases, arabinofuranosidases, and esterases), whereas Enterococcus and Cellulosimicrobium have the potential to degrade oligosaccharides, metabolize xylose and might produce lactic acid through the phosphoketolase (PK) pathway. Based on this evidence, we conclude that our innovative top-down strategy enriched a unique bacterial consortium that could be useful in biotechnological applications, including the development/design of a synthetic bioinoculant to improve silage processes.}, }
@article {pmid35035239, year = {2022}, author = {Chu, LL and Bae, H}, title = {Bacterial endophytes from ginseng and their biotechnological application.}, journal = {Journal of ginseng research}, volume = {46}, number = {1}, pages = {1-10}, pmid = {35035239}, issn = {1226-8453}, abstract = {Ginseng has been well-known as a medicinal plant for thousands of years. Bacterial endophytes ubiquitously colonize the inside tissues of ginseng without any disease symptoms. The identification of bacterial endophytes is conducted through either the internal transcribed spacer region combined with ribosomal sequences or metagenomics. Bacterial endophyte communities differ in their diversity and composition profile, depending on the geographical location, cultivation condition, and tissue, age, and species of ginseng. Bacterial endophytes have a significant effect on the growth of ginseng through indole-3-acetic acid (IAA) and siderophore production, phosphate solubilization, and nitrogen fixation. Moreover, bacterial endophytes can protect ginseng by acting as biocontrol agents. Interestingly, bacterial endophytes isolated from Panax species have the potential to produce ginsenosides and bioactive metabolites, which can be used in the production of food and medicine. The ability of bacterial endophytes to transform major ginsenosides into minor ginsenosides using β-glucosidase is gaining increasing attention as a promising biotechnology. Recently, metabolic engineering has accelerated the possibilities for potential applications of bacterial endophytes in producing beneficial secondary metabolites.}, }
@article {pmid35034639, year = {2022}, author = {Amundson, KK and Borton, MA and Daly, RA and Hoyt, DW and Wong, A and Eder, E and Moore, J and Wunch, K and Wrighton, KC and Wilkins, MJ}, title = {Microbial colonization and persistence in deep fractured shales is guided by metabolic exchanges and viral predation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {5}, pmid = {35034639}, issn = {2049-2618}, support = {EAR-1847684//National Science Foundation/ ; }, abstract = {BACKGROUND: Microbial colonization of subsurface shales following hydraulic fracturing offers the opportunity to study coupled biotic and abiotic factors that impact microbial persistence in engineered deep subsurface ecosystems. Shale formations underly much of the continental USA and display geographically distinct gradients in temperature and salinity. Complementing studies performed in eastern USA shales that contain brine-like fluids, here we coupled metagenomic and metabolomic approaches to develop the first genome-level insights into ecosystem colonization and microbial community interactions in a lower-salinity, but high-temperature western USA shale formation.<br><br>RESULTS: We collected materials used during the hydraulic fracturing process (i.e., chemicals, drill muds) paired with temporal sampling of water produced from three different hydraulically fractured wells in the STACK (Sooner Trend Anadarko Basin, Canadian and Kingfisher) shale play in OK, USA. Relative to other shale formations, our metagenomic and metabolomic analyses revealed an expanded taxonomic and metabolic diversity of microorganisms that colonize and persist in fractured shales. Importantly, temporal sampling across all three hydraulic fracturing wells traced the degradation of complex polymers from the hydraulic fracturing process to the production and consumption of organic acids that support sulfate- and thiosulfate-reducing bacteria. Furthermore, we identified 5587 viral genomes and linked many of these to the dominant, colonizing microorganisms, demonstrating the key role that viral predation plays in community dynamics within this closed, engineered system. Lastly, top-side audit sampling of different source materials enabled genome-resolved source tracking, revealing the likely sources of many key colonizing and persisting taxa in these ecosystems.<br><br>CONCLUSIONS: These findings highlight the importance of resource utilization and resistance to viral predation as key traits that enable specific microbial taxa to persist across fractured shale ecosystems. We also demonstrate the importance of materials used in the hydraulic fracturing process as both a source of persisting shale microorganisms and organic substrates that likely aid in sustaining the microbial community. Moreover, we showed that different physicochemical conditions (i.e., salinity, temperature) can influence the composition and functional potential of persisting microbial communities in shale ecosystems. Together, these results expand our knowledge of microbial life in deep subsurface shales and have important ramifications for management and treatment of microbial biomass in hydraulically fractured wells. Video Abstract.}, }
@article {pmid35034083, year = {2022}, author = {Liaskou, E and Quraishi, MN and Trivedi, PJ}, title = {Mucosal immunity in primary sclerosing cholangitis: from the bowel to bile ducts and back again.}, journal = {Current opinion in gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1097/MOG.0000000000000809}, pmid = {35034083}, issn = {1531-7056}, abstract = {PURPOSE OF REVIEW: In this article, we provide a contemporary overview on PSC pathogenesis, with a specific focus on the role of mucosal immunity.<br><br>RECENT FINDINGS: The extent of enteric dysbiosis in PSC has been extensively quantified, with evidence of reduced bacterial diversity and enrichment of species capable of driving lymphocyte recruitment from the gut to the liver. Integrative pathway-based analysis and metagenomic sequencing indicate a reduction in butyrate-producing species, near absence of bacteria that activate the nuclear bile acid receptor FXR, and depletion of species that regulate the synthesis of vitamin B6 and branched-chain amino acids. Immunotyping of the cellular inflammatory infiltrate has identified a population of intrahepatic naive T cells, with tendency to acquire a Th17 polarisation state, paralleled by heightened responses to pathogen stimulation. Moreover, the search for antigen specificity has revealed the presence of overlapping nucleotide clonotypes across the gut and liver, highlighting the ability to recognize a common pool of epitopes bearing structural similarities across afflicted sites.<br><br>SUMMARY: Understanding the complex mechanisms that underpin mucosal immune responses between the liver and gut will help identify new druggable targets in PSC, centring on gut microbial manipulation, bile acid therapies, and restoration of immune homeostasis.}, }
@article {pmid35033645, year = {2022}, author = {Pang, L and Xu, K and Qi, L and Chatzisymeon, E and Liu, X and Yang, P}, title = {Response behavior of antibiotic resistance genes to zinc oxide nanoparticles in cattle manure thermophilic digestion process: A metagenomic analysis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {126709}, doi = {10.1016/j.biortech.2022.126709}, pmid = {35033645}, issn = {1873-2976}, abstract = {This work investigated the metagenomics-based behavior of antibiotic resistance genes (ARGs) during cattle manure anaerobic digestion with zinc oxide nanoparticles (ZnO NPs) that are commonly used as animal feed additives. The 6.6% decrease in total ARGs abundance while remained unchanged ARGs diversity with ZnO NPs (5 mg/g total solid), suggested ZnO NPs may mitigate ARGs risk by abundance. Also, ZnO NPs affected ARGs with mechanisms specifically of antibiotic inactivation and antibiotic target change, and declined potential hosts' abundance (bacterial genus Ruminiclostridium, Riminococcus, and Paenibacillus) which mainly contributed to the decreased ARGs' abundance. Besides, microbial chemotaxis decreased by 17% with ZnO NPs compared to that without nanoparticles indicated a depression on potential hosts, who could develop the mechanism to adapt to altered digestion conditions, which probably inhibited the ARGs' propagation. These findings are important to promote understanding of the potential ARGs risks in treatments of livestock wastes containing animal feed additives.}, }
@article {pmid35034142, year = {2022}, author = {Tran, HT and Nguyen, HM and Nguyen, TM and Chang, C and Huang, WL and Huang, CL and Chiang, TY}, title = {Microbial Communities Along 2,3,7,8-tetrachlorodibenzodioxin Concentration Gradient in Soils Polluted with Agent Orange Based on Metagenomic Analyses.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35034142}, issn = {1432-184X}, support = {105-2622-B-006 -008 -CC2//Ministry of Science and Technology, Taiwan/ ; }, abstract = {The 2,3,7,8-tetrachlorodibenzodioxin (TCDD), a contaminant in Agent Orange released during the US-Vietnam War, led to a severe environmental crisis. Approximately, 50 years have passed since the end of this war, and vegetation has gradually recovered from the pollution. Soil bacterial communities were investigated by 16S metagenomics in habitats with different vegetation physiognomies in Central Vietnam, namely, forests (S0), barren land (S1), grassland (S2), and developing woods (S3). Vegetation complexity was negatively associated with TCDD concentrations, revealing the reasoning behind the utilization of vegetation physiognomy as an indicator for ecological succession along the gradient of pollutants. Stark changes in bacterial composition were detected between S0 and S1, with an increase in Firmicutes and a decrease in Acidobacteria and Bacteroidetes. Notably, dioxin digesters Arthrobacter, Rhodococcus, Comamonadaceae, and Bacialles were detected in highly contaminated soil (S1). Along the TCDD gradients, following the dioxin decay from S1 to S2, the abundance of Firmicutes and Actinobacteria decreased, while that of Acidobacteria increased; slight changes occurred at the phylum level from S2 to S3. Although metagenomics analyses disclosed a trend toward bacterial communities before contamination with vegetation recovery, non-metric multidimensional scaling analysis unveiled a new trajectory deviating from the native state. Recovery of the bacterial community may have been hindered, as indicated by lower bacterial diversity in S3 compared to S0 due to a significant loss of bacterial taxa and recruitment of fewer colonizers. The results indicate that dioxins significantly altered the soil microbiomes into a state of disorder with a deviating trajectory in restoration.}, }
@article {pmid35033744, year = {2021}, author = {Pérez-Cataluña, A and Chiner-Oms, Á and Cuevas-Ferrando, E and Díaz-Reolid, A and Falcó, I and Randazzo, W and Girón-Guzmán, I and Allende, A and Bracho, MA and Comas, I and Sánchez, G}, title = {Spatial and temporal distribution of SARS-CoV-2 diversity circulating in wastewater.}, journal = {Water research}, volume = {211}, number = {}, pages = {118007}, doi = {10.1016/j.watres.2021.118007}, pmid = {35033744}, issn = {1879-2448}, abstract = {Wastewater-based epidemiology (WBE) has proven to be an effective tool for epidemiological surveillance of SARS-CoV-2 during the current COVID-19 pandemic. Furthermore, combining WBE together with high-throughput sequencing techniques can be useful for the analysis of SARS-CoV-2 viral diversity present in a given sample. The present study focuses on the genomic analysis of SARS-CoV-2 in 76 sewage samples collected during the three epidemiological waves that occurred in Spain from 14 wastewater treatment plants distributed throughout the country. The results obtained demonstrate that the metagenomic analysis of SARS-CoV-2 in wastewater allows the detection of mutations that define the B.1.1.7 lineage and the ability of the technique to anticipate the detection of certain mutations before they are detected in clinical samples. The study proves the usefulness of sewage sequencing to track Variants of Concern that can complement clinical testing to help in decision-making and in the analysis of the evolution of the pandemic.}, }
@article {pmid35033203, year = {2022}, author = {Jankowski, P and Gan, J and Le, T and McKennitt, M and Garcia, A and Yanaç, K and Yuan, Q and Uyaguari-Diaz, M}, title = {Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {3}, pmid = {35033203}, issn = {2524-6372}, support = {322388//Research Start-up Funds, University of Manitoba/ ; 322930//Research Grants Program, University of Manitoba/ ; 322788//The Faculty of Science Collaborative grant, University of Manitoba/ ; }, abstract = {BACKGROUND: Wastewater treatment plants are an essential part of maintaining the health and safety of the general public. However, they are also an anthropogenic source of antibiotic resistance genes. In this study, we characterized the resistome, the distribution of classes 1-3 integron-integrase genes (intI1, intI2, and intI3) as mobile genetic element biomarkers, and the bacterial and phage community compositions in the North End Sewage Treatment Plant in Winnipeg, Manitoba. Samples were collected from raw sewage, returned activated sludge, final effluent, and dewatered sludge. A total of 28 bacterial and viral metagenomes were sequenced over two seasons, fall and winter. Integron-integrase genes, the 16S rRNA gene, and the coliform beta-glucuronidase gene were also quantified during this time period.<br><br>RESULTS: Bacterial classes observed above 1% relative abundance in all treatments were Actinobacteria (39.24% ± 0.25%), Beta-proteobacteria (23.99% ± 0.16%), Gamma-proteobacteria (11.06% ± 0.09%), and Alpha-proteobacteria (9.18 ± 0.04%). Families within the Caudovirales order: Siphoviridae (48.69% ± 0.10%), Podoviridae (23.99% ± 0.07%), and Myoviridae (19.94% ± 0.09%) were the dominant phage observed throughout the NESTP. The most abundant bacterial genera (in terms of average percent relative abundance) in influent, returned activated sludge, final effluent, and sludge, respectively, includes Mycobacterium (37.4%, 18.3%, 46.1%, and 7.7%), Acidovorax (8.9%, 10.8%, 5.4%, and 1.3%), and Polaromonas (2.5%, 3.3%, 1.4%, and 0.4%). The most abundant class of antibiotic resistance in bacterial samples was tetracycline resistance (17.86% ± 0.03%) followed by peptide antibiotics (14.24% ± 0.03%), and macrolides (10.63% ± 0.02%). Similarly, the phage samples contained a higher prevalence of macrolide (30.12% ± 0.30%), peptide antibiotic (10.78% ± 0.13%), and tetracycline (8.69% ± 0.11%) resistance. In addition, intI1 was the most abundant integron-integrase gene throughout treatment (1.14 × 104 gene copies/mL) followed by intI3 (4.97 × 103 gene copies/mL) while intI2 abundance remained low (6.4 × 101 gene copies/mL).<br><br>CONCLUSIONS: Wastewater treatment successfully reduced the abundance of bacteria, DNA phage and antibiotic resistance genes although many antibiotic resistance genes remained in effluent and biosolids. The presence of integron-integrase genes throughout treatment and in effluent suggests that antibiotic resistance genes could be actively disseminating resistance between both environmental and pathogenic bacteria.}, }
@article {pmid34446078, year = {2021}, author = {Alser, M and Rotman, J and Deshpande, D and Taraszka, K and Shi, H and Baykal, PI and Yang, HT and Xue, V and Knyazev, S and Singer, BD and Balliu, B and Koslicki, D and Skums, P and Zelikovsky, A and Alkan, C and Mutlu, O and Mangul, S}, title = {Technology dictates algorithms: recent developments in read alignment.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {249}, pmid = {34446078}, issn = {1474-760X}, support = {R01 HL153122/HL/NHLBI NIH HHS/United States ; K08 HL128867/HL/NHLBI NIH HHS/United States ; U19 AI135964/AI/NIAID NIH HHS/United States ; R01 EB025022/EB/NIBIB NIH HHS/United States ; R01 HL149883/HL/NHLBI NIH HHS/United States ; }, mesh = {*Algorithms ; Computational Biology/*methods ; Genome, Human ; HIV/physiology ; Humans ; Metagenomics ; *Sequence Alignment ; Sulfites ; }, abstract = {Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today's diverse array of alignment methods. We provide a systematic survey of algorithmic foundations and methodologies across 107 alignment methods, for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. We discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology.}, }
@article {pmid34309504, year = {2021}, author = {Wang, Q and Ye, J and Xu, T and Zhou, N and Lu, Z and Ying, J}, title = {Prediction of prokaryotic transposases from protein features with machine learning approaches.}, journal = {Microbial genomics}, volume = {7}, number = {7}, pages = {}, pmid = {34309504}, issn = {2057-5858}, mesh = {Amino Acid Sequence/genetics ; Bacteria/*genetics ; Computational Biology/methods ; DNA Transposable Elements/*genetics ; DNA, Bacterial/*genetics ; Drug Resistance, Bacterial/genetics ; *Machine Learning ; Metagenome/genetics ; Transposases/*genetics ; Virulence Factors/genetics ; }, abstract = {Identification of prokaryotic transposases (Tnps) not only gives insight into the spread of antibiotic resistance and virulence but the process of DNA movement. This study aimed to develop a classifier for predicting Tnps in bacteria and archaea using machine learning (ML) approaches. We extracted a total of 2751 protein features from the training dataset including 14852 Tnps and 14852 controls, and selected 75 features as predictive signatures using the combined mutual information and least absolute shrinkage and selection operator algorithms. By aggregating these signatures, an ensemble classifier that integrated a collection of individual ML-based classifiers, was developed to identify Tnps. Further validation revealed that this classifier achieved good performance with an average AUC of 0.955, and met or exceeded other common methods. Based on this ensemble classifier, a stand-alone command-line tool designated TnpDiscovery was established to maximize the convenience for bioinformaticians and experimental researchers toward Tnp prediction. This study demonstrates the effectiveness of ML approaches in identifying Tnps, facilitating the discovery of novel Tnps in the future.}, }
@article {pmid34126062, year = {2021}, author = {Nooij, S and Ducarmon, QR and Laros, JFJ and Zwittink, RD and Norman, JM and Smits, WK and Verspaget, HW and Keller, JJ and Terveer, EM and Kuijper, EJ and , }, title = {Fecal Microbiota Transplantation Influences Procarcinogenic Escherichia coli in Recipient Recurrent Clostridioides difficile Patients.}, journal = {Gastroenterology}, volume = {161}, number = {4}, pages = {1218-1228.e5}, doi = {10.1053/j.gastro.2021.06.009}, pmid = {34126062}, issn = {1528-0012}, mesh = {Adult ; Aged ; Aged, 80 and over ; Clostridioides difficile/*pathogenicity ; Clostridium Infections/diagnosis/microbiology/*therapy ; Dysbiosis ; Escherichia coli/enzymology/genetics/*growth &amp; development ; Escherichia coli Proteins/genetics/metabolism ; *Fecal Microbiota Transplantation/adverse effects ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Polyketide Synthases/genetics/metabolism ; Reinfection ; Retrospective Studies ; Time Factors ; Treatment Outcome ; }, abstract = {BACKGROUND &amp; AIMS: Patients with multiple recurrent Clostridioides difficile infection (rCDI) have a disturbed gut microbiota that can be restored by fecal microbiota transplantation (FMT). Despite extensive screening, healthy feces donors may carry bacteria in their intestinal tract that could have long-term health effects, such as potentially procarcinogenic polyketide synthase-positive (pks+) Escherichia coli. Here, we aim to determine whether the pks abundance and persistence of pks+E coli is influenced by pks status of the donor feces.<br><br>METHODS: In a cohort of 49 patients with rCDI treated with FMT and matching donor samples-the largest cohort of its kind, to our knowledge-we retrospectively screened fecal metagenomes for pks+E coli and compared the presence of pks in patients before and after treatment and to their respective donors.<br><br>RESULTS: The pks island was more prevalent (P = .026) and abundant (P < .001) in patients with rCDI (pre-FMT, 27 of 49 [55%]; median, 0.46 reads per kilobase per million [RPKM] pks) than in healthy donors (3 of 8 donors [37.5%], 11 of 38 samples [29%]; median, 0.01 RPKM pks). The pks status of patients post-FMT depended on the pks status of the donor suspension with which the patient was treated (P = .046). Particularly, persistence (8 of 9 cases) or clearance (13 of 18) of pks+E coli in pks+ patients was correlated to pks in the donor (P = .004).<br><br>CONCLUSIONS: We conclude that FMT contributes to pks+E coli persistence or eradication in patients with rCDI but that donor-to-patient transmission of pks+E coli is unlikely.}, }
@article {pmid33878301, year = {2021}, author = {Pedersen, MW and De Sanctis, B and Saremi, NF and Sikora, M and Puckett, EE and Gu, Z and Moon, KL and Kapp, JD and Vinner, L and Vardanyan, Z and Ardelean, CF and Arroyo-Cabrales, J and Cahill, JA and Heintzman, PD and Zazula, G and MacPhee, RDE and Shapiro, B and Durbin, R and Willerslev, E}, title = {Environmental genomics of Late Pleistocene black bears and giant short-faced bears.}, journal = {Current biology : CB}, volume = {31}, number = {12}, pages = {2728-2736.e8}, doi = {10.1016/j.cub.2021.04.027}, pmid = {33878301}, issn = {1879-0445}, support = {WT220023/WT_/Wellcome Trust/United Kingdom ; WT207492/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA, Ancient ; DNA, Mitochondrial ; Fossils ; Humans ; Metagenomics ; Phylogeny ; *Ursidae/genetics ; }, abstract = {Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.}, }
@article {pmid35032616, year = {2022}, author = {Matsushima, N and Kretsinger, RH}, title = {Numerous variants of leucine rich repeats in proteins from nucleo-cytoplasmic large DNA viruses.}, journal = {Gene}, volume = {}, number = {}, pages = {146156}, doi = {10.1016/j.gene.2021.146156}, pmid = {35032616}, issn = {1879-0038}, abstract = {Leucine rich repeats (LRRs) occurring in tandem are 20 - 29 amino acids long. Eleven LRR types have been recognized. Sequence features of LRRs from viruses were investigated using over 600 LRR proteins from 89 species. Directly before, metagenome data of nucleo-cytoplasmic large dsDNA viruses (NCLDVs) have been published; the 2,074 NCLDVs encode 199,021 proteins. From the NCLDVs 547 LRR proteins were identified and 502 were used for analysis. A comprehensive analysis of TpLRR and FNIP that belong to an LRR type was first performed. The repeating unit lengths (RULs) in five types are 19 residues which is the shortest among all LRRs. The RULs of eight LRR types including FNIP are one to five residues shorter than those of the known, corresponding LRR types. The conserved hydrophobic residues such as Leu, Val or Ile in the consensus sequences are frequently substituted by cysteine at one or two positions. Four unique LRR motifs that are different from those identified previously are observed. The present study enhances the previous result that the sequence novelty is a general feature of viral LRR proteins. An evolutionary scenario of short or unique LRR was discussed.}, }
@article {pmid35032364, year = {2022}, author = {Nie, J and Yang, L and Huang, L and Gao, L and Young, KH and Le Grange, JM and Yang, X and Wei, J and Xiao, M and Zhou, J}, title = {Infection complications in febrile chimeric antigen receptor (CAR)-T recipients during the peri-CAR-T cell treatment period examined using metagenomic next-generation sequencing (mNGS).}, journal = {Cancer communications (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1002/cac2.12260}, pmid = {35032364}, issn = {2523-3548}, support = {82070217//National Natural Science Foundation of China/ ; 81873427//National Natural Science Foundation of China/ ; 81770211//National Natural Science Foundation of China/ ; 81670152//National Natural Science Foundation of China/ ; 81700145//National Natural Science Foundation of China/ ; 81830008//Key Program of the National Natural Science Foundation of China/ ; 81630006//Key Program of the National Natural Science Foundation of China/ ; CXPJJH12000009-113//CHEN XIAO-PING Foundation for the Development of Science and Technology of Hubei Province/ ; }, }
@article {pmid35032344, year = {2022}, author = {Rasmussen, JA and Villumsen, KR and von Gersdorff Jørgensen, L and Forberg, T and Zuo, S and Kania, PW and Buchmann, K and Kristiansen, K and Bojesen, AM and Limborg, MT}, title = {Integrative analyses of probiotics, pathogenic infections, and host immune response highlight the importance of gut microbiota in understanding disease recovery in rainbow trout (Oncorhynchus mykiss).}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15433}, pmid = {35032344}, issn = {1365-2672}, abstract = {AIMS: Given the pivotal role played by the gut microbiota in regulating the host immune system, interest has arisen in the possibility of controlling fish health by modulating the gut microbiota. Hence, the need for a better understanding of the host-microbiota interactions after disease responses to optimise the use of probiotics to strengthen disease resilience and recovery.<br><br>METHODS AND RESULTS: We tested the effects of a probiotic feed additive in rainbow trout and challenged the fish with the causative agent for enteric redmouth disease, Yersinia ruckeri. We evaluated the survival, host immune gene expression and on the gut microbiota composition. Results revealed that provision of probiotics and exposure to Y. ruckeri induced immune gene expression in the host associated with changes in the gut microbiota. Subsequently, infection with Y. ruckeri had very little effect on microbiota composition when probiotics were applied, indicating that probiotics increased stabilisation of the microbiota. Our analysis revealed potential biomarkers for monitoring infection status and fish health. Finally, we used modelling approaches to decipher interactions between gut bacteria and the host immune gene responses, indicating removal of endogenous bacteria elicited by non-specific immune responses.<br><br>CONCLUSIONS: We discuss the relevance of these results emphasising the importance of host-microbiota interactions, including the protective potential of the gut microbiota in disease responses.<br><br>Our results highlight the functional consequences of probiotic-induced changes in the gut microbiota and the resulting host immune response.}, }
@article {pmid35030982, year = {2022}, author = {Tan, R and Jin, M and Shao, Y and Yin, J and Li, H and Chen, T and Shi, D and Zhou, S and Li, J and Yang, D}, title = {High-sugar, high-fat, and high-protein diets promote antibiotic resistance gene spreading in the mouse intestinal microbiota.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2022442}, doi = {10.1080/19490976.2021.2022442}, pmid = {35030982}, issn = {1949-0984}, abstract = {Diet can not only provide nutrition for intestinal microbiota, it can also remodel them. However, is unclear whether and how diet affects the spread of antibiotic resistance genes (ARGs) in the intestinal microbiota. Therefore, we employed selected high-sugar, high-fat, high-protein, and normal diets to explore the effect. The results showed that high-sugar, high-fat, and high-protein diets promoted the amplification and transfer of exogenous ARGs among intestinal microbiota, and up-regulated the expression of trfAp and trbBp while significantly altered the intestinal microbiota and its metabolites. Inflammation-related products were strongly correlated with the spread of ARGs, suggesting the intestinal microenvironment after diet remodeling might be conducive to the spreading of ARGs. This may be attributed to changes in bacterial membrane permeability, the SOS response, and bacterial composition and diversity caused by diet-induced inflammation. In addition, acceptor bacteria (zygotes) screened by flow cytometry were mostly Proteobacteria, Firmicutes and Actinobacteria, and most were derived from dominant intestinal bacteria remodeled by diet, indicating that the transfer of ARGs was closely linked to diet, and had some selectivity. Metagenomic results showed that the gut resistance genome could be affected not only by diet, but by exogenous antibiotic resistant bacteria (ARB). Many ARG markers coincided with bacterial markers in diet groups. Therefore, dominant bacteria in different diets are important hosts of ARGs in specific dietary environments, but the many pathogenic bacteria present may cause serious harm to human health.}, }
@article {pmid35030359, year = {2022}, author = {Xu, X and Chen, H and Hu, J and Zheng, T and Zhang, R and Zhong, H and Gao, Q and Sun, W and Chen, Q and Ni, J}, title = {Unveil the role of dissolved and sedimentary metal(loid)s on bacterial communities and metal resistance genes (MRGs) in an urban river of the Qinghai-Tibet Plateau.}, journal = {Water research}, volume = {211}, number = {}, pages = {118050}, doi = {10.1016/j.watres.2022.118050}, pmid = {35030359}, issn = {1879-2448}, abstract = {Though metal resistance genes (MRGs) are of global concern in aquatic ecosystems, the underlying factors responsible for MRGs dissemination, especially in urban rivers on the vulnerable Qinghai-Tibet Plateau, are rarely known. Here, we collected 64 samples including water and sediments during the wet and dry seasons and effluents from six wastewater treatment plants (WWTPs) during the dry season and measured 50 metal(loid)s, 60 bacterial phyla, and 259 MRGs. We observed the distinct difference of metal(loid)s, bacterial communities, and MRGs between water and sediments and the great seasonal changes in metal(loid)s and bacterial communities instead of MRGs. Thirty-one metal(loid)s were detectable in the water, with relatively low concentrations and no significant effects on the planktonic bacterial communities and MRGs. Interestingly, the WWTPs effluent partially promoted the prevalence of dissolved metal(loid)s, bacterial communities, and MRGs along the river. In the sediments, the average concentrations of 17 metal(loid)s exceeded their corresponding background levels in this region and strongly influenced the bacterial communities and the MRGs. Sedimentary Hg and Cd, mainly sourced from the intensive animal husbandry, were the major pollutants causing ecological risks and largely shaped their corresponding resistomes. Moreover, we found that bacterial communities predominantly determined the variation of MRGs in both water and sediments. Metagenome-assembled genomes further reveals the widespread co-occurrence of MRGs and antibiotic resistance genes (ARGs) in MRG hosts. Our study highlighted the concern of effluents discharged from WWTPs and emphasized the importance of controlling the anthropogenic inputs of sedimentary metal(loid)s in the plateau river ecosystems.}, }
@article {pmid35030192, year = {2022}, author = {El Mouzan, M and Assiri, A and Al Sarkhy, A and Alasmi, M and Saeed, A and Al-Hussaini, A and AlSaleem, B and Al Mofarreh, M}, title = {Viral dysbiosis in children with new-onset celiac disease.}, journal = {PloS one}, volume = {17}, number = {1}, pages = {e0262108}, doi = {10.1371/journal.pone.0262108}, pmid = {35030192}, issn = {1932-6203}, abstract = {Viruses are common components of the intestinal microbiome, modulating host bacterial metabolism and interacting with the immune system, with a possible role in the pathogenesis of immune-mediated diseases such as celiac disease (CeD). The objective of this study was to characterize the virome profile in children with new-onset CeD. We used metagenomic analysis of viral DNA in mucosal and fecal samples from children with CeD and controls and performed sequencing using the Nextera XT library preparation kit. Abundance log2 fold changes were calculated using differential expression and linear discriminant effect size. Shannon alpha and Bray-Curtis beta diversity were determined. A total of 40 children with CeD and 39 controls were included. We found viral dysbiosis in both fecal and mucosal samples. Examples of significantly more abundant species in fecal samples of children with CeD included Human polyomavirus 2, Enterobacteria phage mEpX1, and Enterobacteria phage mEpX2; whereas less abundant species included Lactococcus phages ul36 and Streptococcus phage Abc2. In mucosal samples however, no species were significantly associated with CeD. Shannon alpha diversity was not significantly different between CeD and non-CeD groups and Bray-Curtis beta diversity showed no significant separation between CeD and non-CeD samples in either mucosal or stool samples, whereas separation was clear in all samples. We identified significant viral dysbiosis in children with CeD, suggesting a potential role in the pathogenesis of CeD indicating the need for further studies.}, }
@article {pmid35029658, year = {2022}, author = {Takada, N and Takasugi, M and Nonaka, Y and Kamiya, T and Takemura, K and Satoh, J and Ito, S and Fujimoto, K and Uematsu, S and Yoshida, K and Morita, T and Nakamura, H and Uezumi, A and Ohtani, N}, title = {Galectin-3 promotes the adipogenic differentiation of PDGFRα+ cells and ectopic fat formation in regenerating muscle.}, journal = {Development (Cambridge, England)}, volume = {}, number = {}, pages = {}, doi = {10.1242/dev.199443}, pmid = {35029658}, issn = {1477-9129}, support = {19H04002//Japan Society for the Promotion of Science (JSPS)/ ; //Takeda Science Foundation/ ; }, abstract = {Worldwide prevalence of obesity is associated with the increase of lifestyle-related diseases. The accumulation of intermuscular adipose tissue (IMAT) is considered a major problem whereby obesity leads to sarcopenia and metabolic disorders and thus is a promising target for treating these pathological conditions. However, whereas obesity-associated IMAT is suggested to originate from PDGFRα+ mesenchymal progenitors, processes underlying their adipogenesis remain largely unexplored. Here, we comprehensively investigated intra- and extracellular changes associated with these processes using single-cell RNA sequencing (scRNA-Seq) and mass spectrometry. Our scRNA-Seq analysis identified a small PDGFRα+ cell population in obese mice directed strongly toward adipogenesis. Proteomic analysis showed that the appearance of this cell population is accompanied by an increase in galectin-3 in interstitial environments, which was found to activate adipogenic PPARγ signals in PDGFRα+ cells. Moreover, IMAT formation during muscle regeneration was significantly suppressed in galectin-3 KO mice. Our findings, together with these multi-omics datasets, could unravel microenvironmental networks during muscle regeneration highlighting possible therapeutic targets against IMAT formation in obesity.}, }
@article {pmid35028627, year = {2021}, author = {Pfavayi, LT and Sibanda, EN and Baker, S and Woolhouse, M and Mduluza, T and Mutapi, F}, title = {Fungal allergic sensitisation in young rural Zimbabwean children: Gut mycobiome and seroreactivity characteristics.}, journal = {Current research in microbial sciences}, volume = {2}, number = {}, pages = {100082}, doi = {10.1016/j.crmicr.2021.100082}, pmid = {35028627}, issn = {2666-5174}, abstract = {Background: The prevalence of allergic diseases has increased over the last few decades, with sensitisation to fungal allergens and gut microbiome dysbiosis implicated in this trend. The fungal community in the gut (mycobiome) has yet to be characterised and related to fungal allergic sensitisation. Thus, we characterised the gut mycobiome and related it to fungal sensitisation and seroreactivity among Zimbabwean children. We further determined the effect of host age, sex, Schistosoma haematobium infection and mycobiome composition on fungal sensitisation and seroreactivity.<br><br>Methods: Using shotgun metagenomic sequencing, we characterised the gut microbiome of stool samples of 116 preschool aged children (PSAC) (≤5 years old, 57(49.1%) male and 59 (50.9%) female). Sensitisation to common fungi in Zimbabwe was assessed using skin prick tests (SPTs). Allergen-specific IgM, IgA, IgG, IgE and IgG4 antibodies were quantified by ELISA. We analysed the relationship between fungal genera and SPT reactivity by ANOVA; fungal genera and IgE antibody reactivity by linear regression; variation in mycobiome abundance with host and environmental factors by PERMANOVA; SPT reactivity and host and environmental factors by logistic regression; seroreactivity and host and environmental factors by ANOVA.<br><br>Results: The mycobiome formed <1% of the sequenced gut microbiome and 228 fungal genera were identified. The most abundant genera detected were Protomyces, Taphrina, and Aspergillus. S.haematobium infection had a significant effect on fungal genera. Prevalence of SPT sensitisation to ≥1 fungal species was 96%, and individuals were frequently sensitised to Saccharomyces cerevisiae. Antibodies were detected in 100% of the population. There was no relationship between mycobiome abundance and IgE titres or IgE/IgG4 ratios for each fungal species; no significant differences between SPT reactivity and abundance of fungal species except for S. cerevisiae; and fungal seroreactivity did not significantly differ with age. There were some sex (m>f for, Epicoccum nigrum and Penicillium chrysogenum) and SPT reactivity -related differences in seroreactivity.<br><br>Conclusion: This is the first comprehensive characterisation of gut mycobiome and fungal allergic sensitisation of rural children in Zimbabwe. Although reported allergic disease is low there is a high percentage of sensitisation. Further studies with larger populations are required to understand the role of the mycobiome in allergic diseases.}, }
@article {pmid35028498, year = {2022}, author = {Li, J and Li, J and Yu, Y and Wang, R and Zhou, M and Lu, L}, title = {Pneumocystis pneumonia and rheumatic disease: diagnostic potential of circulating microbial cell-free DNA sequencing.}, journal = {Rheumatology advances in practice}, volume = {6}, number = {1}, pages = {rkab105}, doi = {10.1093/rap/rkab105}, pmid = {35028498}, issn = {2514-1775}, abstract = {Objectives: The aim of this study was to explore the clinical utility of circulating microbial cell-free DNA (cfDNA) sequencing as a non-invasive approach for diagnosis of Pneumocystis jirovecii pneumonia (PJP) in immunocompromised patients with rheumatic disease (RD).<br><br>Methods: The study included 72 RD patients with suspected lung infections admitted to Renji hospital. Eighteen individuals were diagnosed with PJP, and 54 patients without PJP were enrolled as the control group. All patients had undergone pulmonary CT scans, and blood and respiratory tract specimens had been subjected to metagenomic next-generation sequencing (mNGS) and conventional microbiological tests. The clinical and laboratory parameters were collected, and the efficacy of circulating microbial cfDNA of P. jirovecii was evaluated.<br><br>Results: Of the 18 patients with PJP, the average age was 53.0 years, and the median time between RD diagnosis and PJP presentation was 126.0 days (interquartile range 84.0-176.3 days). Low circulating CD4+ cell counts and a lack of PJP prophylaxis were observed in the patients. Metagenomic NGS of circulating microbial cfDNA was performed in 69 patients, including 15 cases with PJP and 54 controls. Twelve (80%) of 15 analysed blood samples contained P. jirovecii sequences in the PJP group, with P. jirovecii not detected among controls. There was a significant difference between PJP and non-PJP groups (P < 0.001), with a sensitivity of 83.3% and specificity of 100% when using plasma cfDNA sequencing. Higher β-D-glucan levels were found in patients with positive results for P. jirovecii in plasma cfDNA sequencing.<br><br>Conclusion: Metagenomic NGS of circulating microbial cfDNA is a potential tool for diagnosis of PJP in RD patients.}, }
@article {pmid35027725, year = {2022}, author = {Muñoz-Gómez, SA and Susko, E and Williamson, K and Eme, L and Slamovits, CH and Moreira, D and López-García, P and Roger, AJ}, title = {Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {35027725}, issn = {2397-334X}, support = {735923LPI//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; GBMF9739//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; ALTF 21-2020//European Molecular Biology Organization (EMBO)/ ; }, abstract = {Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional heterogeneity. We applied this site-and-branch-heterogeneous model (MAM60 + GFmix) to a considerably expanded dataset that comprises 108 mitochondrial proteins of alphaproteobacterial origin, and novel metagenome-assembled genomes from microbial mats, microbialites and sediments. The MAM60 + GFmix model fits the data much better and agrees with analyses of compositionally homogenized datasets with conventional site-heterogenous models. The consilience of evidence thus suggests that mitochondria are sister to the Alphaproteobacteria to the exclusion of MarineProteo1 and Magnetococcia. We also show that the ancestral presence of the crista-developing mitochondrial contact site and cristae organizing system (a mitofilin-domain-containing Mic60 protein) in mitochondria and the Alphaproteobacteria only supports their close relationship.}, }
@article {pmid35027090, year = {2022}, author = {Rajala, P and Cheng, DQ and Rice, SA and Lauro, FM}, title = {Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {4}, pmid = {35027090}, issn = {2049-2618}, abstract = {BACKGROUND: Metal corrosion in seawater has been extensively studied in surface and shallow waters. However, infrastructure is increasingly being installed in deep-sea environments, where extremes of temperature, salinity, and high hydrostatic pressure increase the costs and logistical challenges associated with monitoring corrosion. Moreover, there is currently only a rudimentary understanding of the role of microbially induced corrosion, which has rarely been studied in the deep-sea. We report here an integrative study of the biofilms growing on the surface of corroding mooring chain links that had been deployed for 10 years at ~2 km depth and developed a model of microbially induced corrosion based on flux-balance analysis.<br><br>METHODS: We used optical emission spectrometry to analyze the chemical composition of the mooring chain and energy-dispersive X-ray spectrometry coupled with scanning electron microscopy to identify corrosion products and ultrastructural features. The taxonomic structure of the microbiome was determined using shotgun metagenomics and was confirmed by 16S amplicon analysis and quantitative PCR of the dsrB gene. The functional capacity was further analyzed by generating binned, genomic assemblies and performing flux-balance analysis on the metabolism of the dominant taxa.<br><br>RESULTS: The surface of the chain links showed intensive and localized corrosion with structural features typical of microbially induced corrosion. The microbiome on the links differed considerably from that of the surrounding sediment, suggesting selection for specific metal-corroding biofilms dominated by sulfur-cycling bacteria. The core metabolism of the microbiome was reconstructed to generate a mechanistic model that combines biotic and abiotic corrosion. Based on this metabolic model, we propose that sulfate reduction and sulfur disproportionation might play key roles in deep-sea corrosion.<br><br>CONCLUSIONS: The corrosion rate observed was higher than what could be expected from abiotic corrosion mechanisms under these environmental conditions. High corrosion rate and the form of corrosion (deep pitting) suggest that the corrosion of the chain links was driven by both abiotic and biotic processes. We posit that the corrosion is driven by deep-sea sulfur-cycling microorganisms which may gain energy by accelerating the reaction between metallic iron and elemental sulfur. The results of this field study provide important new insights on the ecophysiology of the corrosion process in the deep sea.}, }
@article {pmid34772759, year = {2021}, author = {Kardos, M and Armstrong, EE and Fitzpatrick, SW and Hauser, S and Hedrick, PW and Miller, JM and Tallmon, DA and Funk, WC}, title = {The crucial role of genome-wide genetic variation in conservation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {48}, pages = {}, pmid = {34772759}, issn = {1091-6490}, support = {RL5 GM118990/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; Ecosystem ; Genetic Fitness/genetics ; Genetic Variation/*genetics ; Genetics ; Genetics, Population/methods ; Genome/*genetics ; Genomics ; Inbreeding ; Metagenomics/methods ; Population Dynamics/*trends ; }, abstract = {The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.}, }
@article {pmid33926534, year = {2021}, author = {Kobras, CM and Fenton, AK and Sheppard, SK}, title = {Next-generation microbiology: from comparative genomics to gene function.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {123}, pmid = {33926534}, issn = {1474-760X}, support = {MR/S009280/1/MRC_/Medical Research Council/United Kingdom ; MR/M501608/1/MRC_/Medical Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; DNA Transposable Elements ; *Gene Expression Regulation ; Genetic Association Studies ; Genetic Fitness ; Genetic Variation ; Genome-Wide Association Study/methods ; *Genomics/methods ; Metagenome ; Metagenomics/methods ; Microbiological Techniques/*trends ; Microbiology/*trends ; Mutagenesis, Insertional ; }, abstract = {Microbiology is at a turning point in its 120-year history. Widespread next-generation sequencing has revealed genetic complexity among bacteria that could hardly have been imagined by pioneers such as Pasteur, Escherich and Koch. This data cascade brings enormous potential to improve our understanding of individual bacterial cells and the genetic basis of phenotype variation. However, this revolution in data science cannot replace established microbiology practices, presenting the challenge of how to integrate these new techniques. Contrasting comparative and functional genomic approaches, we evoke molecular microbiology theory and established practice to present a conceptual framework and practical roadmap for next-generation microbiology.}, }
@article {pmid35026256, year = {2022}, author = {Wang, J and Zhang, Y and Ding, Y and Song, H and Liu, T}, title = {Analysis of microbial community resistance mechanisms in groundwater contaminated with SAs and high NH4+-Fe-Mn.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {153036}, doi = {10.1016/j.scitotenv.2022.153036}, pmid = {35026256}, issn = {1879-1026}, abstract = {The resistance mechanism of microbial communities in contaminated groundwater under the combined stress of sulfonamide antibiotics (SAs), NH4+, and Fe-Mn exceeding the standard levels was studied in an agricultural area along the Songhua River in Northeast China with developed livestock and poultry breeding. Representative points were selected in the study area to explore the response of environmental parameters and microbial communities, and microscopic experiments with different SA concentrations were conducted with background groundwater. The results showed a complex relationship between microbial communities and environmental factors. The environmental factors SM, SM2, SMX, DOC, NO3-, Fe, Mn, and HCO3- significantly affected the microbial community, with SMX, DOC, and Mn having the greatest effect. Three types of antibiotics with similar properties had different effects on the microbial community, and these effects were not simply additive or superimposed. After adding SAs, Proteobacteria with multi-resistance (99.85%) became the dominant phylum, and Acinetobacter (98.68%) became the dominant genus with SA resistance. SAs have a significant influence on bacterial chemotaxis, transporters, substance transport, and metabolism. Microorganisms resist the influence of SAs via a series of resistance mechanisms, such as enhancing the synthesis of relevant enzymes, generating new biochemical reactions, and reducing the transport of harmful substances through cell membranes. We also found that the proportion of exogenous compound degradation and metabolism-related functional genes in the presence of high SA concentrations increased significantly, which may be related to the degradation of SAs by microorganisms.}, }
@article {pmid35026253, year = {2022}, author = {Shi, L and Zhang, J and Lu, T and Zhang, K}, title = {Metagenomics revealed the mobility and hosts of antibiotic resistance genes in typical pesticide wastewater treatment plants.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {153033}, doi = {10.1016/j.scitotenv.2022.153033}, pmid = {35026253}, issn = {1879-1026}, abstract = {Pesticide showed a crucial selective pressure of antibiotic resistance genes (ARGs) in the environmental dimension, especially in the pesticide wastewater treatment process, where the information on the mobility and hosts of ARGs was very important but limited. This study tried to clarify the mobile antibiotic resistome and ARG hosts in three typical pesticide wastewater treatment plants (PWWTPs) through metagenomics. Results showed that ARGs associated with antibiotic efflux and multi-drug resistance generally dominated in the PWWTPs, and the relative abundance of ARGs was generally higher in the water phase than that in sludge phase. The mobile antibiotic resistome accounted for 43.6% ± 16.2% and 44.8% ± 18.0% of the total relative abundance of ARGs in the water phase and sludge phase, respectively. The tnpA, IS91 and intI1 were the dominant mobile genetic elements (MGEs) closely associated with ARGs. MCR-5 and MCR-9 were first identified in the PWWTPs and located together with the tnpA, tnpA2 and int2. The potential human pathogens belonging to Citrobacter, Pseudomonas, Enterobacter, Acinetobacter, and Kluyvern were the major ARG hosts in the PWWTPs. Statistical analysis indicated that microbial community contributed the most to the occurrence of antibiotic resistome, and the reduction of the major ARG hosts was crucial from the perspective of ARGs control.}, }
@article {pmid35024477, year = {2022}, author = {Ahlinder, J and Svedberg, AL and Nystedt, A and Dryselius, R and Jacobsson, K and Hägglund, M and Brindefalk, B and Forsman, M and Ottoson, J and Troell, K}, title = {Use of metagenomic microbial source tracking to investigate the source of a foodborne outbreak of cryptosporidiosis.}, journal = {Food and waterborne parasitology}, volume = {26}, number = {}, pages = {e00142}, doi = {10.1016/j.fawpar.2021.e00142}, pmid = {35024477}, issn = {2405-6766}, abstract = {Cryptosporidium is a protozoan parasite of global public health importance that causes gastroenteritis in a variety of vertebrate hosts, with many human outbreaks reported yearly, often from ingestion of contaminated water or food. Despite the major public health implications, little is typically known about sources of contamination of disease outbreaks caused by Cryptosporidium. Here, we study a national foodborne outbreak resulted from infection with Cryptosporidium parvum via romaine lettuce, with the main goal to trace the source of the parasite. To do so, we combined traditional outbreak investigation methods with molecular detection and characterization methods (i.e. PCR based typing, amplicon and shotgun sequencing) of romaine lettuce samples collected at the same farm from which the contaminated food was produced. Using 18S rRNA typing, we detected C. parvum in two out of three lettuce samples, which was supported by detections in the metagenome analysis. Microbial source tracking analysis of the lettuce samples suggested sewage water as a likely source of the contamination, albeit with some uncertainty. In addition, the high degree of overlap in bacterial species content with a public human gut microbial database corroborated the source tracking results. The combination of traditional and molecular based methods applied here is a promising tool for future source tracking investigations of food- and waterborne outbreaks of Cryptosporidium spp. and can help to control and mitigate contamination risks.}, }
@article {pmid35024099, year = {2022}, author = {Pettersen, VK and Antunes, LCM and Dufour, A and Arrieta, MC}, title = {Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {274-286}, doi = {10.1016/j.csbj.2021.12.012}, pmid = {35024099}, issn = {2001-0370}, abstract = {Humans have a long-standing coexistence with microorganisms. In particular, the microbial community that populates the human gastrointestinal tract has emerged as a critical player in governing human health and disease. DNA and RNA sequencing techniques that map taxonomical composition and genomic potential of the gut community have become invaluable for microbiome research. However, deriving a biochemical understanding of how activities of the gut microbiome shape host development and physiology requires an expanded experimental design that goes beyond these approaches. In this review, we explore advances in high-throughput techniques based on liquid chromatography-mass spectrometry. These omics methods for the identification of proteins and metabolites have enabled direct characterisation of gut microbiome functions and the crosstalk with the host. We discuss current metaproteomics and metabolomics workflows for producing functional profiles, the existing methodological challenges and limitations, and recent studies utilising these techniques with a special focus on early life gut microbiome.}, }
@article {pmid35024091, year = {2022}, author = {Pust, MM and Tümmler, B}, title = {Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {175-186}, doi = {10.1016/j.csbj.2021.12.008}, pmid = {35024091}, issn = {2001-0370}, abstract = {The default removal of low-abundance (rare) taxa from microbial community analyses may lead to an incomplete picture of the taxonomic and functional microbial potential within the human habitat. Publicly available shotgun metagenomics data of healthy children and children with cystic fibrosis (CF) were reanalysed to study the development of the rare species biosphere, which was here defined by either the 15th, 25th or 35th species abundance percentile. We found that healthy children contained an age-independent network of abundant (core) and rare species with both entities being essential in maintaining the network structure. The protein sequence usage for more than 100 bacterial metabolic pathways differed between the core and rare species biosphere. In CF children, the background structure was underdeveloped and random forest bootstrapping based on all constituents of the early airway metagenome and host-associated factors indicated that rare taxa were the most important variables in deciding whether a child was healthy or suffered from the life-limiting CF disease. Attempts failed to make the age-independent CF network as robust as the healthy structure when an increasing number of bacterial taxa from the healthy network was incorporated into the CF structure by computer-based model simulations. However, the transfer of a key combination of taxa from the healthy to the CF network structure with high species diversity and low species dominance, correlated with a more robust CF network and a topological approximation of CF and healthy graph structures. Rothia mucilaginosa, Streptococci and rare species were essential in improving the underdeveloped CF network.}, }
@article {pmid35023810, year = {2022}, author = {Udayan, S and Stamou, P and Crispie, F and Hickey, A and Floyd, AN and Hsieh, CS and Cotter, PD and O'Sullivan, O and Melgar, S and O'Toole, PW and Newberry, RD and Rossini, V and Nally, K}, title = {Identification of Gut Bacteria such as Lactobacillus johnsonii that Disseminate to Systemic Tissues of Wild Type and MyD88-/- Mice.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2007743}, doi = {10.1080/19490976.2021.2007743}, pmid = {35023810}, issn = {1949-0984}, abstract = {In healthy hosts the gut microbiota is restricted to gut tissues by several barriers some of which require MyD88-dependent innate immune sensor pathways. Nevertheless, some gut taxa have been reported to disseminate to systemic tissues. However, the extent to which this normally occurs during homeostasis in healthy organisms is still unknown. In this study, we recovered viable gut bacteria from systemic tissues of healthy wild type (WT) and MyD88-/- mice. Shotgun metagenomic-sequencing revealed a marked increase in the relative abundance of L. johnsonii in intestinal tissues of MyD88-/- mice compared to WT mice. Lactobacillus johnsonii was detected most frequently from multiple systemic tissues and at higher levels in MyD88-/- mice compared to WT mice. Viable L. johnsonii strains were recovered from different cell types sorted from intestinal and systemic tissues of WT and MyD88-/- mice. L. johnsonii could persist in dendritic cells and may represent murine immunomodulatory endosymbionts.}, }
@article {pmid35022515, year = {2022}, author = {Qin, F and Du, S and Zhang, Z and Ying, H and Wu, Y and Zhao, G and Yang, M and Zhao, Y}, title = {Newly identified HMO-2011-type phages reveal genomic diversity and biogeographic distributions of this marine viral group.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {35022515}, issn = {1751-7370}, support = {41706173//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076105//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Viruses play critical roles in influencing biogeochemical cycles and adjusting host mortality, population structure, physiology, and evolution in the ocean. Marine viral communities are composed of numerous genetically distinct subfamily/genus-level viral groups. Among currently identified viral groups, the HMO-2011-type group is known to be dominant and broadly distributed. However, only four HMO-2011-type cultivated representatives that infect marine SAR116 and Roseobacter strains have been reported to date, and the genetic diversity, potential hosts, and ecology of this group remain poorly elucidated. Here, we present the genomes of seven HMO-2011-type phages that were isolated using four Roseobacter strains and one SAR11 strain, as well as additional 207 HMO-2011-type metagenomic viral genomes (MVGs) identified from various marine viromes. Phylogenomic and shared-gene analyses revealed that the HMO-2011-type group is a subfamily-level group comprising at least 10 discernible genus-level subgroups. Moreover, >2000 HMO-2011-type DNA polymerase sequences were identified, and the DNA polymerase phylogeny also revealed that the HMO-2011-type group contains diverse subgroups and is globally distributed. Metagenomic read-mapping results further showed that most HMO-2011-type phages are prevalent in global oceans and display distinct geographic distributions, with the distribution of most HMO-2011-type phages being associated with temperature. Lastly, we found that members in subgroup IX, represented by pelagiphage HTVC033P, were among the most abundant HMO-2011-type phages, which implies that SAR11 bacteria are crucial hosts for this viral group. In summary, our findings substantially expand current knowledge regarding the phylogenetic diversity, evolution, and distribution of HMO-2011-type phages, highlighting HMO-2011-type phages as major ecological agents that can infect certain key bacterial groups.}, }
@article {pmid35022403, year = {2022}, author = {Bornemann, TLV and Adam, PS and Turzynski, V and Schreiber, U and Figueroa-Gonzalez, PA and Rahlff, J and Köster, D and Schmidt, TC and Schunk, R and Krauthausen, B and Probst, AJ}, title = {Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {284}, pmid = {35022403}, issn = {2041-1723}, abstract = {Earth's mantle releases 38.7 ± 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere.}, }
@article {pmid35021874, year = {2022}, author = {Wang, Y and Tian, S and Wu, N and Liu, W and Li, L and Wang, X}, title = {Differential microbial communities in paddy soils between Guiyang plateaus and Chengdu basins drive the incidence of rice bacterial diseases.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-09-21-1974-RE}, pmid = {35021874}, issn = {0191-2917}, abstract = {Southwest China has the most complex rice-growing regions in China. With great differences in topography, mainly consisting of basins and plateaus, ecological factors in above region differ greatly. In this study, bulk paddy soils collected from a long-term rice field in Chengdu (basins) and in Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared more than 70% of the dominant genera (abundance > 1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively related with the higher incidence of rice bacterial foot rot in Guiyang, while temperature had a greater effect on soil microbial functions and positively related with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.}, }
@article {pmid35021085, year = {2022}, author = {Gulyaeva, A and Garmaeva, S and Ruigrok, RAAA and Wang, D and Riksen, NP and Netea, MG and Wijmenga, C and Weersma, RK and Fu, J and Vila, AV and Kurilshikov, A and Zhernakova, A}, title = {Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts.}, journal = {Cell reports}, volume = {38}, number = {2}, pages = {110204}, doi = {10.1016/j.celrep.2021.110204}, pmid = {35021085}, issn = {2211-1247}, abstract = {The crAss-like phages are a diverse group of related viruses that includes some of the most abundant viruses of the human gut. To explore their diversity and functional role in human population and clinical cohorts, we analyze gut metagenomic data collected from 1,950 individuals from the Netherlands. We identify 1,556 crAss-like phage genomes, including 125 species-level and 32 genus-level clusters absent from the reference databases used. Analysis of their genomic features shows that closely related crAss-like phages can possess strikingly divergent regions responsible for transcription, presumably acquired through recombination. Prediction of crAss-like phage hosts points primarily to bacteria of the phylum Bacteroidetes, consistent with previous reports. Finally, we explore the temporal stability of crAss-like phages over a 4-year period and identify associations between the abundance of crAss-like phages and several human phenotypes, including depletion of crAss-like phages in inflammatory bowel disease patients.}, }
@article {pmid35021078, year = {2022}, author = {Hu, D and Fuller, NR and Caterson, ID and Holmes, AJ and Reeves, PR}, title = {Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome.}, journal = {Cell reports}, volume = {38}, number = {2}, pages = {110239}, doi = {10.1016/j.celrep.2021.110239}, pmid = {35021078}, issn = {2211-1247}, abstract = {Gut microbiome is of major interest due to its close relationship to health and disease. Bacteria usually vary in gene content, leading to functional variations within species, so resolution higher than species-level methods is needed for ecological and clinical relevance. We design a protocol to identify strains in selected species with high discrimination and in high numbers by amplicon sequencing of the flagellin gene. We apply the protocol to fecal samples from a human diet trial, targeting Escherichia coli. Across the 119 samples from 16 individuals, there are 1,532 amplicon sequence variants (ASVs), but only 32 ASVs are dominant in one or more fecal samples, despite frequent dominant strain turnover. Major strains in an intestine are found to be commonly accompanied by a large number of satellite cells, and many are identified as potential extraintestinal pathogens. The protocol could be used to track epidemics or investigate the intra- or inter-host diversity of pathogens.}, }
@article {pmid35020455, year = {2022}, author = {Cao, Y and Zhang, B and Greer, CW and Lee, K and Cai, Q and Song, X and Tremblay, J and Zhu, Z and Dong, G and Chen, B}, title = {Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {aem0215121}, doi = {10.1128/aem.02151-21}, pmid = {35020455}, issn = {1098-5336}, abstract = {The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1500 mL) microcosms without nutrients addition using low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved into the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic based Metagenome Assembled Genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. Importance In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days) whereas exerting insignificant effects in the late stage (50 days), from both substances removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation, and clarified their degradation and antioxidation mechanisms. The findings would help to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit, and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response.}, }
@article {pmid35020412, year = {2022}, author = {Du, Y and Laperriere, SM and Fuhrman, J and Sun, F}, title = {Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/cmb.2021.0439}, pmid = {35020412}, issn = {1557-8666}, abstract = {High-throughput chromosome conformation capture (Hi-C) has recently been applied to natural microbial communities and revealed great potential to study multiple genomes simultaneously. Several extraneous factors may influence chromosomal contacts rendering the normalization of Hi-C contact maps essential for downstream analyses. However, the current paucity of metagenomic Hi-C normalization methods and the ignorance for spurious interspecies contacts weaken the interpretability of the data. Here, we report on two types of biases in metagenomic Hi-C experiments: explicit biases and implicit biases, and introduce HiCzin, a parametric model to correct both types of biases and remove spurious interspecies contacts. We demonstrate that the normalized metagenomic Hi-C contact maps by HiCzin result in lower biases, higher capability to detect spurious contacts, and better performance in metagenomic contig clustering.}, }
@article {pmid35019890, year = {2022}, author = {Zhu, J and Xia, H and Tang, R and Ng, TK and Yao, F and Liao, X and Zhang, Q and Ke, X and Shi, T and Chen, H}, title = {Metagenomic Next-generation Sequencing Detects Pathogens in Endophthalmitis Patients.}, journal = {Retina (Philadelphia, Pa.)}, volume = {}, number = {}, pages = {}, doi = {10.1097/IAE.0000000000003406}, pmid = {35019890}, issn = {1539-2864}, abstract = {PURPOSE: To investigate the utility of metagenomic next-generation sequencing (mNGS) in identifying the pathogens in endophthalmitis.<br><br>METHODS: In this prospective study, 36 cases of endophthalmitis were recruited. All patients received surgical treatment and intraocular drug lavage. The samples of vitreous or aqueous humor were extracted for mNGS and microbiological culture. The diagnostic performance of pathogens was compared between mNGS and culture.<br><br>RESULTS: The positive rates of mNGS and culture were 88.89% (32/36) and 27.78% (10/36), respectively. There was a statistically significant difference between mNGS and culture (χ2=27.657, P <0.01). Staphylococcus epidermidis, Streptococcus pneumoniae and Klebsiella pneumoniae were the most pathogenic bacteria in traumatic, postoperative, and endogenous endophthalmitis respectively. The concordance of pathogen identified by mNGS and culture was 70% for culture-positive cases. Antibiotic resistance genes were identified in 9 cases. There was a marginal correlation between the final visual acuity and the microbial sequence read (rs=0.498, P=0.05).<br><br>CONCLUSIONS: mNGS has a higher positive rate of identifying pathogens in endophthalmitis than culture. It can also provide information on antibiotic resistance and visual prognosis. However, caution must be taken when interpreting the results of mNGS because they may be not concordant with culture.}, }
@article {pmid35019699, year = {2022}, author = {Jeon, S and Kim, H and Kim, J and Seol, D and Jo, J and Choi, Y and Cho, S and Kim, H}, title = {Positive Effect of Lactobacillus acidophilus EG004 on Cognitive Ability of Healthy Mice by Fecal Microbiome Analysis Using Full-Length 16S-23S rRNA Metagenome Sequencing.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0181521}, doi = {10.1128/spectrum.01815-21}, pmid = {35019699}, issn = {2165-0497}, abstract = {Evidence for the concept of the "gut-brain axis" (GBA) has risen. Many types of research demonstrated the mechanism of the GBA and the effect of probiotic intake. Although many studies have been reported, most were focused on neurodegenerative disease and, it is still not clear what type of bacterial strains have positive effects. We designed an experiment to discover a strain that positively affects brain function, which can be recognized through changes in cognitive processes using healthy mice. The experimental group consisted of a control group and three probiotic consumption groups, namely, Lactobacillus acidophilus, Lacticaseibacillus paracasei, and Lacticaseibacillus rhamnosus. Three experimental groups fed probiotics showed an improved cognitive ability by cognitive-behavioral tests, and the group fed on L. acidophilus showed the highest score. To provide an understanding of the altered microbial composition effect on the brain, we performed full 16S-23S rRNA sequencing using Nanopore, and operational taxonomic units (OTUs) were identified at species level. In the group fed on L. acidophilus, the intestinal bacterial ratio of Firmicutes and Proteobacteria phyla increased, and the bacterial proportions of 16 species were significantly different from those of the control group. We estimated that the positive results on the cognitive behavioral tests were due to the increased proportion of the L. acidophilus EG004 strain in the subjects' intestines since the strain can produce butyrate and therefore modulate neurotransmitters and neurotrophic factors. We expect that this strain expands the industrial field of L. acidophilus and helps understand the mechanism of the gut-brain axis. IMPORTANCE Recently, the concept of the "gut-brain axis" has risen and suggested that microbes in the GI tract affect the brain by modulating signal molecules. Although many pieces of research were reported in a short period, a signaling mechanism and the effects of a specific bacterial strain are still unclear. Besides, since most of the research was focused on neurodegenerative disease, the study with a healthy animal model is still insufficient. In this study, we show using a healthy animal model that a bacterial strain (Lactobacillus acidophilus EG004) has a positive effect on mouse cognitive ability. We experimentally verified an improved cognitive ability by cognitive behavioral tests. We performed full 16S-23S rRNA sequencing using a Nanopore MinION instrument and provided the gut microbiome composition at the species level. This microbiome composition consisted of candidate microbial groups as a biomarker that shows positive effects on cognitive ability. Therefore, our study suggests a new perspective for probiotic strain use applicable for various industrialization processes.}, }
@article {pmid35019688, year = {2022}, author = {Lin, B and Wang, M and Gao, R and Ye, Z and Yu, Y and He, W and Qiao, N and Ma, Z and Ji, C and Shi, C and Zhou, X and Wang, Y and Zeng, F and Zhang, L and Gong, W and Cao, Z and Zhou, P and Melnikov, V and Ye, H and Li, Y and Zhang, Z and He, M and Qin, H and Zhang, Y}, title = {Characteristics of Gut Microbiota in Patients with GH-Secreting Pituitary Adenoma.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0042521}, doi = {10.1128/spectrum.00425-21}, pmid = {35019688}, issn = {2165-0497}, abstract = {Prior study has demonstrated that gut microbiota at the genus level is significantly altered in patients with growth hormone (GH)-secreting pituitary adenoma (GHPA). Yet, no studies exist describing the state of gut microbiota at species level in GHPA. We performed a study using 16S rRNA amplicon sequencing in a cohort of patients with GH-secreting pituitary adenoma (GHPA, n = 28) and healthy controls (n = 67). Among them, 9 patients and 10 healthy controls were randomly chosen and enrolled in metagenomics shotgun sequencing, generating 280,426,512 reads after aligning to NCBI GenBank DataBase to acquire taxa information at the species level. Weighted UniFrac analysis revealed that microbial diversity was notably decreased in patients with GHPA, consistent with a previous study. With 16S rRNA sequencing, after correction for false-discovery rate (FDR), rank-sum test at the genus level revealed that the relative abundance of Oscillibacter and Enterobacter was remarkably increased in patients and Blautia and Romboutsia genera predominated in the controls, augmented by additional LEfSe (linear discriminant analysis effect size) analysis. As for further comparison at the species level with metagenomics sequencing, rank-sum test together with LEfSe analysis confirmed the enrichment of Alistipes shahii and Odoribacter splanchnicus in the patient group. Notably, LEfSe analysis with metagenomics also demonstrated that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND, derived from Enterobacter, were both significantly enriched in patients. Functional analysis showed that amino acid metabolism pathway was remarkably enriched in GHPA, while carbohydrate metabolism pathway was notably enriched in controls. Further, significant positive correlations were observed between Enterobacter and baseline insulin-like growth factor 1 (IGF-1), indicating that Enterobacter may be strongly associated with GH/IGF-1 axis in GHPA. Our data extend our insight into the GHPA microbiome, which may shed further light on GHPA pathogenesis and facilitate the exploration of novel therapeutic targets based on microbiota manipulation. IMPORTANCE Dysbiosis of gut microbiota is associated not only with intestinal disorders but also with numerous extraintestinal diseases. Growth hormone-secreting pituitary adenoma (GHPA) is an insidious disease with persistent hypersecretion of GH and IGF-1, causing increased morbidity and mortality. Researches have reported that the GH/IGF-1 axis exerts its own influence on the intestinal microflora. Here, the results showed that compared with healthy controls, GHPA patients not only decreased the alpha diversity of the intestinal flora but also significantly changed their beta diversity. Further, metagenomics shotgun sequencing in the present study exhibited that Enterobacter sp. DC1 and Enterobacter sp. 940 PEND were enriched in patients. Also, we were pleasantly surprised to find that the Enterobacter genus was strongly positively correlated with baseline IGF-1 levels. Collectively, our work provides the first glimpse of the dysbiosis of the gut microbiota at species level, providing a better understanding of the pathophysiological process of GHPA.}, }
@article {pmid35019675, year = {2022}, author = {Lombardino, J and Bijlani, S and Singh, NK and Wood, JM and Barker, R and Gilroy, S and Wang, CCC and Venkateswaran, K}, title = {Genomic Characterization of Potential Plant Growth-Promoting Features of Sphingomonas Strains Isolated from the International Space Station.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0199421}, doi = {10.1128/spectrum.01994-21}, pmid = {35019675}, issn = {2165-0497}, abstract = {In an ongoing microbial tracking investigation of the International Space Station (ISS), several Sphingomonas strains were isolated. Based on the 16S rRNA gene sequence, phylogenetic analysis identified the ISS strains as Sphingomonas sanguinis (n = 2) and one strain isolated from the Kennedy Space Center cleanroom (used to assemble various Mars mission spacecraft components) as Sphingomonas paucimobilis. Metagenomic sequence analyses of different ISS locations identified 23 Sphingomonas species. An abundance of shotgun metagenomic reads were detected for S. sanguinis in the location from where the ISS strains were isolated. A complete metagenome-assembled genome was generated from the shotgun reads metagenome, and its comparison with the whole-genome sequences (WGS) of the ISS S. sanguinis isolates revealed that they were highly similar. In addition to the phylogeny, the WGS of these Sphingomonas strains were compared with the WGS of the type strains to elucidate genes that can potentially aid in plant growth promotion. Furthermore, the WGS comparison of these strains with the well-characterized Sphingomonas sp. LK11, an arid desert strain, identified several genes responsible for the production of phytohormones and for stress tolerance. Production of one of the phytohormones, indole-3-acetic acid, was further confirmed in the ISS strains using liquid chromatography-mass spectrometry. Pathways associated with phosphate uptake, metabolism, and solubilization in soil were conserved across all the S. sanguinis and S. paucimobilis strains tested. Furthermore, genes thought to promote plant resistance to abiotic stress, including heat/cold shock response, heavy metal resistance, and oxidative and osmotic stress resistance, appear to be present in these space-related S. sanguinis and S. paucimobilis strains. Characterizing these biotechnologically important microorganisms found on the ISS and harnessing their key features will aid in the development of self-sustainable long-term space missions in the future. IMPORTANCE Sphingomonas is ubiquitous in nature, including the anthropogenically contaminated extreme environments. Members of the Sphingomonas genus have been identified as potential candidates for space biomining beyond earth. This study describes the isolation and identification of Sphingomonas members from the ISS, which are capable of producing the phytohormone indole-3-acetic acid. Microbial production of phytohormones will help future in situ studies, grow plants beyond low earth orbit, and establish self-sustainable life support systems. Beyond phytohormone production, stable genomic elements of abiotic stress resistance, heavy metal resistance, and oxidative and osmotic stress resistance were identified, rendering the ISS Sphingomonas isolate a strong candidate for biotechnology-related applications.}, }
@article {pmid35019672, year = {2022}, author = {Sun, Z and Zhang, M and Li, M and Bhaskar, Y and Zhao, J and Ji, Y and Cui, H and Zhang, H and Sun, Z}, title = {Interactions between Human Gut Microbiome Dynamics and Sub-Optimal Health Symptoms during Seafaring Expeditions.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0092521}, doi = {10.1128/spectrum.00925-21}, pmid = {35019672}, issn = {2165-0497}, abstract = {During long ocean voyages, crew members are subject to complex pressures from their living and working environment, which lead to chronic diseases-like sub-optimal health status. Although the association between dysbiotic gut microbiome and chronic diseases has been broadly reported, the correlation between the sub-optimal health status and gut microbiome remains elusive. Here, the health status of 77 crew members (20-35 years old Chinese, male) during a 135-day sea expedition was evaluated using the shotgun metagenomics of stool samples and health questionnaires taken before and after the voyage. We found five core symptoms (e.g., abnormal defecation frequency, insomnia, poor sleep quality, nausea, and overeating) in 55 out of 77 crew members suffering from sub-optimal health status, and this was termed "seafaring syndrome" (SS) in this study. Significant correlation was found between the gut microbiome and SS rather than any single symptom. For example, SS was proven to be associated with individual perturbation in the gut microbiome, and the microbial dynamics between SS and non-SS samples were different during the voyage. Moreover, the microbial signature for SS was identified using the variation of 19 bacterial species and 26 gene families. Furthermore, using a Random Forest model, SS was predicted with high accuracy (84.4%, area under the concentration-time curve = 0.91) based on 28 biomarkers from pre-voyage samples, and the prediction model was further validated by another 30-day voyage cohort (accuracy = 83.3%). The findings in this study provide insights to help us discover potential predictors or even therapeutic targets for dysbiosis-related diseases. IMPORTANCE Systemic and chronic diseases are important health problems today and have been proven to be strongly associated with dysbiotic gut microbiome. Studying the association between the gut microbiome and sub-optimal health status of humans in extreme environments (such as ocean voyages) will give us a better understanding of the interactions between observable health signs and a stable versus dysbiotic gut microbiome states. In this paper, we illustrated that ocean voyages could trigger different symptoms for different crew member cohorts due to individual differences; however, the co-occurrence of high prevalence symptoms indicated widespread perturbation of the gut microbiome. By investigating the microbial signature and gut microbiome dynamics, we demonstrated that such sub-optimal health status can be predicted even before the voyage. We termed this phenomenon as "seafaring syndrome." This study not only provides the potential strategy for health management in extreme environments but also can assist the prediction of other dysbiosis-related diseases.}, }
@article {pmid35019069, year = {2022}, author = {Herlinger, AL and Monteiro, FLL and D'arc, M and Moreira, FRR and Westgarth, HJ and Galliez, RM and Mariani, D and da Costa, LJ and de Almeida, LGP and Voloch, CM and ,  and Melo, ASO and Aguiar, RS and Dos Santos, AFA and Castiñeiras, TMPP and de Vasconcelos, ATR and João Filho, EC and Escosteguy, CC and Ferreira Junior, ODC and Tanuri, A and Higa, LM}, title = {Identification and characterisation of SARS-CoV-2 and Human alphaherpesvirus 1 from a productive coinfection in a fatal COVID-19 case.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {116}, number = {}, pages = {e210176}, doi = {10.1590/0074-02760210176}, pmid = {35019069}, issn = {1678-8060}, abstract = {BACKGROUND: During routine Coronavirus disease 2019 (COVID-19) diagnosis, an unusually high viral load was detected by reverse transcription real-time polymerase chain reaction (RT-qPCR) in a nasopharyngeal swab sample collected from a patient with respiratory and neurological symptoms who rapidly succumbed to the disease. Therefore we sought to characterise the infection.<br><br>OBJECTIVES: We aimed to determine and characterise the etiological agent responsible for the poor outcome.<br><br>METHODS: Classical virological methods, such as plaque assay and plaque reduction neutralisation test combined with amplicon-based sequencing, as well as a viral metagenomic approach, were performed to characterise the etiological agents of the infection.<br><br>FINDINGS: Plaque assay revealed two distinct plaque phenotypes, suggesting either the presence of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains or a productive coinfection of two different species of virus. Amplicon-based sequencing did not support the presence of any SARS-CoV-2 genetic variants that would explain the high viral load and suggested the presence of a single SARS-CoV-2 strain. Nonetheless, the viral metagenomic analysis revealed that Coronaviridae and Herpesviridae were the predominant virus families within the sample. This finding was confirmed by a plaque reduction neutralisation test and PCR.<br><br>MAIN CONCLUSIONS: We characterised a productive coinfection of SARS-CoV-2 and Herpes simplex virus 1 (HSV-1) in a patient with severe symptoms that succumbed to the disease. Although we cannot establish the causal relationship between the coinfection and the severity of the clinical case, this work serves as a warning for future studies focused on the interplay between SARS-CoV-2 and HSV-1 coinfection and COVID-19 severity.}, }
@article {pmid35017197, year = {2022}, author = {Belda, E and Voland, L and Tremaroli, V and Falony, G and Adriouch, S and Assmann, KE and Prifiti, E and Aron-Wisnewsky, J and Debédat, J and Le Roy, T and Nielsen, T and Amouyal, C and André, S and Andreelli, F and Blüher, M and Chakaroun, R and Chilloux, J and Coelho, LP and Dao, MC and Das, P and Fellahi, S and Forslund, S and Galleron, N and Hansen, TH and Holmes, B and Ji, B and Krogh Pedersen, H and Le, P and Le Chatelier, E and Lewinter, C and Mannerås-Holm, L and Marquet, F and Myridakis, A and Pelloux, V and Pons, N and Quinquis, B and Rouault, C and Roume, H and Salem, JE and Sokolovska, N and Søndertoft, NB and Touch, S and Vieira-Silva, S and ,  and Galan, P and Holst, J and Gøtze, JP and Køber, L and Vestergaard, H and Hansen, T and Hercberg, S and Oppert, JM and Nielsen, J and Letunic, I and Dumas, ME and Stumvoll, M and Pedersen, OB and Bork, P and Ehrlich, SD and Zucker, JD and Bäckhed, F and Raes, J and Clément, K}, title = {Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2021-325753}, pmid = {35017197}, issn = {1468-3288}, abstract = {OBJECTIVES: Gut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear. We examined the human gut microbiome's functional composition in healthy metabolic state and the most severe states of obesity and type 2 diabetes within the MetaCardis cohort. We focused on the role of B vitamins and B7/B8 biotin for regulation of host metabolic state, as these vitamins influence both microbial function and host metabolism and inflammation.<br><br>DESIGN: We performed metagenomic analyses in 1545 subjects from the MetaCardis cohorts and different murine experiments, including germ-free and antibiotic treated animals, faecal microbiota transfer, bariatric surgery and supplementation with biotin and prebiotics in mice.<br><br>RESULTS: Severe obesity is associated with an absolute deficiency in bacterial biotin producers and transporters, whose abundances correlate with host metabolic and inflammatory phenotypes. We found suboptimal circulating biotin levels in severe obesity and altered expression of biotin-associated genes in human adipose tissue. In mice, the absence or depletion of gut microbiota by antibiotics confirmed the microbial contribution to host biotin levels. Bariatric surgery, which improves metabolism and inflammation, associates with increased bacterial biotin producers and improved host systemic biotin in humans and mice. Finally, supplementing high-fat diet-fed mice with fructo-oligosaccharides and biotin improves not only the microbiome diversity, but also the potential of bacterial production of biotin and B vitamins, while limiting weight gain and glycaemic deterioration.<br><br>CONCLUSION: Strategies combining biotin and prebiotic supplementation could help prevent the deterioration of metabolic states in severe obesity.<br><br>TRIAL REGISTRATION NUMBER: NCT02059538.}, }
@article {pmid35017031, year = {2022}, author = {Boeri, L and Donnaloja, F and Campanile, M and Sardelli, L and Tunesi, M and Fusco, F and Giordano, C and Albani, D}, title = {Using integrated meta-omics to appreciate the role of the gut microbiota in epilepsy.}, journal = {Neurobiology of disease}, volume = {}, number = {}, pages = {105614}, doi = {10.1016/j.nbd.2022.105614}, pmid = {35017031}, issn = {1095-953X}, abstract = {The way the human microbiota may modulate neurological pathologies is a fascinating matter of research. Epilepsy is a common neurological disorder, which has been largely investigated in correlation with microbiota health and function. However, the mechanisms that regulate this apparent connection are scarcely defined, and extensive effort has been conducted to understand the role of microbiota in preventing and reducing epileptic seizures. Intestinal bacteria seem to modulate the seizure frequency mainly by releasing neurotransmitters and inflammatory mediators. In order to elucidate the complex microbial contribution to epilepsy pathophysiology, integrated meta-omics could be pivotal. In fact, the combination of two or more meta-omics approaches allows a multifactorial study of microbial activity within the frame of disease or drug treatments. In this review, we provide information depicting and supporting the use of multi-omics to study the microbiota-epilepsy connection. We described different meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics), focusing on current technical challenges in stool collection procedures, sample extraction methods and data processing. We further discussed the current advantages and limitations of using the integrative approach of multi-omics in epilepsy investigations.}, }
@article {pmid35016998, year = {2022}, author = {Franck, M and de Toro-Martín, J and Varin, TV and Garneau, V and Pilon, G and Roy, D and Couture, P and Couillard, C and Marette, A and Vohl, MC}, title = {Raspberry consumption: identification of distinct immune-metabolic response profiles by whole blood transcriptome profiling.}, journal = {The Journal of nutritional biochemistry}, volume = {}, number = {}, pages = {108946}, doi = {10.1016/j.jnutbio.2022.108946}, pmid = {35016998}, issn = {1873-4847}, abstract = {Numerous studies have reported that diets rich in phenolic compounds are beneficial to immune-metabolic health, yet these effects are heterogeneous and the underlying mechanisms are poorly understood. To investigate the inter-individual variability of the immune-metabolic response to raspberry consumption, whole-blood RNAseq data from 24 participants receiving 280g/day of raspberries for 8 weeks were used for the identification of responsiveness subgroups by using partial least squares-discriminant analysis (PLSDA) and hierarchical clustering. Transcriptomic-based clustering regrouped participants into two distinct subgroups of 13 and 11 participants, so-called responders and non-responders, respectively. Following raspberry consumption, a significant decrease in triglycerides, cholesterol and C-reactive protein levels were found in responders, as compared to non-responders. Two major gene expression components of 100 and 220 genes were identified by sparse PLSDA as those better discriminating responders from non-responders, and functional analysis identified pathways related to cytokine production, leukocyte activation and immune response as significantly enriched with most discriminant genes. As compared to non-responders, the plasma lipidomic profile of responders was characterized by a significant decrease in triglycerides and an increase in phosphatidylcholines following raspberry consumption. Prior to the intervention, a distinct metagenomic profile was identified by PLSDA between responsiveness subgroups, and the Firmicutes-to-Bacteroidota ratio was found significantly lower in responders, as compared to non-responders. Findings point to this transcriptomic-based clustering approach as a suitable tool to identify distinct responsiveness subgroups to raspberry consumption. This approach represents a promising framework to tackle the issue of inter-individual variability in the understanding of the impact of foods on immune-metabolic health.}, }
@article {pmid35016706, year = {2022}, author = {Bolte, EE and Moorshead, D and Aagaard, KM}, title = {Maternal and early life exposures and their potential to influence development of the microbiome.}, journal = {Genome medicine}, volume = {14}, number = {1}, pages = {4}, pmid = {35016706}, issn = {1756-994X}, support = {HD091731//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; DK089201//National Institutes of Health (US)/ ; }, abstract = {At the dawn of the twentieth century, the medical care of mothers and children was largely relegated to family members and informally trained birth attendants. As the industrial era progressed, early and key public health observations among women and children linked the persistence of adverse health outcomes to poverty and poor nutrition. In the time hence, numerous studies connecting genetics ("nature") to public health and epidemiologic data on the role of the environment ("nurture") have yielded insights into the importance of early life exposures in relation to the occurrence of common diseases, such as diabetes, allergic and atopic disease, cardiovascular disease, and obesity. As a result of these parallel efforts in science, medicine, and public health, the developing brain, immune system, and metabolic physiology are now recognized as being particularly vulnerable to poor nutrition and stressful environments from the start of pregnancy to 3 years of age. In particular, compelling evidence arising from a diverse array of studies across mammalian lineages suggest that modifications to our metagenome and/or microbiome occur following certain environmental exposures during pregnancy and lactation, which in turn render risk of childhood and adult diseases. In this review, we will consider the evidence suggesting that development of the offspring microbiome may be vulnerable to maternal exposures, including an analysis of the data regarding the presence or absence of a low-biomass intrauterine microbiome.}, }
@article {pmid34838108, year = {2021}, author = {Lin, D and Zheng, X and Sanogo, B and Ding, T and Sun, X and Wu, Z}, title = {Bacterial composition of midgut and entire body of laboratory colonies of Aedes aegypti and Aedes albopictus from Southern China.}, journal = {Parasites &amp; vectors}, volume = {14}, number = {1}, pages = {586}, pmid = {34838108}, issn = {1756-3305}, support = {2020YFC1200100//the National Key R&amp;D Program of China/ ; 2016YFC1200500//the National Key R&amp;D Program of China/ ; 2019A1515012068//Natural Science Foundation of Guangdong Province/ ; 2020A1515010896//Natural Science Foundation of Guangdong Province/ ; 2021A1515010976//Natural Science Foundation of Guangdong Province/ ; 82072308//the National Natural Science Foundation of China/ ; 82002168//the National Natural Science Foundation of China/ ; 20201192//the 6th Nuclear Energy R&amp;D Project/ ; B12003//The 111 Project/ ; }, mesh = {Aedes/*microbiology ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; China ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Laboratories ; Metagenomics ; Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are invasive mosquito species and significantly impact human health in southern China. Microbiota are confirmed to affect the development and immunity of mosquitoes. However, scientists have focused more on midgut microbiota of female mosquitoes and bacterial differences between female and male Aedes mosquitoes. The relationship between the midgut and entire body microbiota of Aedes is unclear. In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.<br><br>METHODS: In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.<br><br>RESULTS: A total of 341 OTUs were identified, showing that Proteobacteria was the dominant phylum and Methylobacterium the dominant genus in both Aedes aegypti and Aedes albopictus. The bacterial diversity and community structures of the entire bodies were similar between males and females in both Aedes aegypti and Aedes albopictus. Conversely, the bacterial compositions of male and female Aedes aegypti and Aedes albopictus were significantly different. NMDS analysis, UPGMA analysis, diversity indices and OTU distribution demonstrated that compositions and structures in midgut microbiota were similar but significantly different in the entire bodies of Aedes aegypti and Aedes albopictus. Functional prediction analysis showed that metabolism and environmental information processing were the dominant KEGG pathways at level 1. Our study showed that there were significantly different level 2 and 3 KEGG pathways in the midgut microbiota (16 level 2 and 24 level 3) and the entire bodies (33 level 2 and 248 level 3) between female Aedes albopictus and Aedes Aegypti.<br><br>CONCLUSIONS: Our findings that Aedes aegypti and Aedes albopictus reared in the same laboratory harbor a similar gut bacterial microbiome but different entire body microbiota imply that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype, but the entire body microbiota is more genetically determined. Our findings improved the understanding of the microbiota in the entire and partial tissues of Aedes mosquitoes.}, }
@article {pmid34030623, year = {2021}, author = {Méndez-Salazar, EO and Vázquez-Mellado, J and Casimiro-Soriguer, CS and Dopazo, J and Çubuk, C and Zamudio-Cuevas, Y and Francisco-Balderas, A and Martínez-Flores, K and Fernández-Torres, J and Lozada-Pérez, C and Pineda, C and Sánchez-González, A and Silveira, LH and Burguete-García, AI and Orbe-Orihuela, C and Lagunas-Martínez, A and Vazquez-Gomez, A and López-Reyes, A and Palacios-González, B and Martínez-Nava, GA}, title = {Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {27}, number = {1}, pages = {50}, pmid = {34030623}, issn = {1528-3658}, mesh = {Biodiversity ; Computational Biology/methods ; *Dysbiosis ; *Gastrointestinal Microbiome ; Gout/etiology/*metabolism/pathology ; Humans ; *Metagenome ; *Metagenomics/methods ; Protein Interaction Mapping ; Protein Interaction Maps ; Uric Acid/*metabolism ; }, abstract = {OBJECTIVE: To evaluate the taxonomic composition of the gut microbiome in gout patients with and without tophi formation, and predict bacterial functions that might have an impact on urate metabolism.<br><br>METHODS: Hypervariable V3-V4 regions of the bacterial 16S rRNA gene from fecal samples of gout patients with and without tophi (n = 33 and n = 25, respectively) were sequenced and compared to fecal samples from 53 healthy controls. We explored predictive functional profiles using bioinformatics in order to identify differences in taxonomy and metabolic pathways.<br><br>RESULTS: We identified a microbiome characterized by the lowest richness and a higher abundance of Phascolarctobacterium, Bacteroides, Akkermansia, and Ruminococcus_gnavus_group genera in patients with gout without tophi when compared to controls. The Proteobacteria phylum and the Escherichia-Shigella genus were more abundant in patients with tophaceous gout than in controls. Fold change analysis detected nine genera enriched in healthy controls compared to gout groups (Bifidobacterium, Butyricicoccus, Oscillobacter, Ruminococcaceae_UCG_010, Lachnospiraceae_ND2007_group, Haemophilus, Ruminococcus_1, Clostridium_sensu_stricto_1, and Ruminococcaceae_UGC_013). We found that the core microbiota of both gout groups shared Bacteroides caccae, Bacteroides stercoris ATCC 43183, and Bacteroides coprocola DSM 17136. These bacteria might perform functions linked to one-carbon metabolism, nucleotide binding, amino acid biosynthesis, and purine biosynthesis. Finally, we observed differences in key bacterial enzymes involved in urate synthesis, degradation, and elimination.<br><br>CONCLUSION: Our findings revealed that taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.}, }
@article {pmid35016010, year = {2022}, author = {Murchie, TJ and Karpinski, E and Eaton, K and Duggan, AT and Baleka, S and Zazula, G and MacPhee, RDE and Froese, D and Poinar, HN}, title = {Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2021.12.023}, pmid = {35016010}, issn = {1879-0445}, abstract = {Traditionally, paleontologists have relied on the morphological features of bones and teeth to reconstruct the evolutionary relationships of extinct animals.1 In recent decades, the analysis of ancient DNA recovered from macrofossils has provided a powerful means to evaluate these hypotheses and develop novel phylogenetic models.2 Although a great deal of life history data can be extracted from bones, their scarcity and associated biases limit their information potential. The paleontological record of Beringia3-the unglaciated areas and former land bridge between northeast Eurasia and northwest North America-is relatively robust thanks to its perennially frozen ground favoring fossil preservation.4,5 However, even here, the macrofossil record is significantly lacking in small-bodied fauna (e.g., rodents and birds), whereas questions related to migration and extirpation, even among well-studied taxa, remain crudely resolved. The growing sophistication of ancient environmental DNA (eDNA) methods have allowed for the identification of species within terrestrial/aquatic ecosystems,6-12 in paleodietary reconstructions,13-19 and facilitated genomic reconstructions from cave contexts.8,20-22 Murchie et al.6,23 used a capture enrichment approach to sequence a diverse range of faunal and floral DNA from permafrost silts deposited during the Pleistocene-Holocene transition.24 Here, we expand on their work with the mitogenomic assembly and phylogenetic placement of Equus caballus (caballine horse), Bison priscus (steppe bison), Mammuthus primigenius (woolly mammoth), and Lagopus lagopus (willow ptarmigan) eDNA from multiple permafrost cores spanning the last 30,000 years. We identify a diverse metagenomic spectra of Pleistocene fauna and identify the eDNA co-occurrence of distinct Eurasian and American mitogenomic lineages.}, }
@article {pmid35015746, year = {2022}, author = {Ghare, S and Singhal, R and Bryant, V and Gautam, S and Tirumala, CC and Srisailam, PK and Reyes-Vega, A and Ghooray, D and McClain, CJ and Hoffman, K and Petrosino, J and Bryant, K and Govind, V and Cohen, R and Cook, RL and Barve, S}, title = {Age-Associated Gut Dysbiosis, Marked by Loss of Butyrogenic Potential, Correlates With Altered Plasma Tryptophan Metabolites in Older People Living With HIV.}, journal = {Journal of acquired immune deficiency syndromes (1999)}, volume = {89}, number = {Suppl 1}, pages = {S56-S64}, doi = {10.1097/QAI.0000000000002866}, pmid = {35015746}, issn = {1944-7884}, abstract = {BACKGROUND: Imbalance in tryptophan (TRP) metabolism and its neuroactive metabolites, serotonin and kynurenine (KYN), is a known pathogenic mechanism underlying neurocognitive impairment. Gut microbiota plays an important role in TRP metabolism, and the production of these neuroactive molecules affects neurocognitive function. Although both HIV infection and normal aging independently induce gut dysbiosis and influence TRP metabolism, their interactive effects on compositional/functional changes in gut microbiota and consequent alterations in TRP metabolites remain largely undetermined.<br><br>METHODS: Older people living with HIV infection (PLWH, aged 50-70 years, n = 22) were enrolled in this cross-sectional pilot study. Metagenomic analysis of fecal microbiome using 16S Ribosomal ribonucleic acid gene sequencing and metabolomics analysis of plasma using mass spectrometry with a reverse-phase iquid chromatography tandem mass spectrometry were performed. Statistical analyses included the univariate linear regression and Spearman correlation analyses.<br><br>RESULTS: Age-associated changes in plasma levels of key neuroactive TRP metabolites, serotonin and KYN, were seen in PLWH. Specifically, we observed age-dependent decreases in serotonin and increases in KYN and KYN-to-TRP ratio, indicative of dysfunctional TRP metabolism. Furthermore, the gut dysbiosis seen in older PLWH is characterized by a reduction of Firmicutes/Bacteroidetes ratio and butyrate-producing microbial families Lachnospiraceae and Lactobacillaceae. Of importance, correspondent with gut dysbiosis, increasing age was significantly associated with decreased plasma butyrate levels, which in turn correlated positively with serotonin and negatively with KYN/TRP ratio.<br><br>CONCLUSIONS: Age-dependent gut microbial dysbiosis distinguished by a decrease in butyrogenic potential is a key pathogenic feature associated with the shift in TRP metabolism from serotonin to KYN in older PLWH.}, }
@article {pmid35015311, year = {2022}, author = {Negrey, JD and Mitani, JC and Wrangham, RW and Otali, E and Reddy, RB and Pappas, TE and Grindle, KA and Gern, JE and Machanda, ZP and Muller, MN and Langergraber, KE and Emery Thompson, M and Goldberg, TL}, title = {Viruses associated with ill health in wild chimpanzees.}, journal = {American journal of primatology}, volume = {}, number = {}, pages = {e23358}, doi = {10.1002/ajp.23358}, pmid = {35015311}, issn = {1098-2345}, support = {BCS-1355014//National Science Foundation/ ; BCS-1613392//National Science Foundation/ ; BCS-1613393//National Science Foundation/ ; DGE-1256260//National Science Foundation/ ; NCS-FO 1926653//National Science Foundation/ ; R01AG049395/NH/NIH HHS/United States ; //Nacey-Maggioncalda Foundation/ ; //Wenner-Gren Foundation/ ; 9742-15//National Geographic Society/ ; 9824-15//National Geographic Society/ ; //Leakey Foundation/ ; //University of New Mexico/ ; //University of Wisconsin-Madison/ ; //Boston University/ ; //University of Michigan/ ; }, abstract = {Viral infection is a major cause of ill health in wild chimpanzees (Pan troglodytes), but most evidence to date has come from conspicuous disease outbreaks with high morbidity and mortality. To examine the relationship between viral infection and ill health during periods not associated with disease outbreaks, we conducted a longitudinal study of wild eastern chimpanzees (P. t. schweinfurthii) in the Kanyawara and Ngogo communities of Kibale National Park, Uganda. We collected standardized, observational health data for 4 years and then used metagenomics to characterize gastrointestinal viromes (i.e., all viruses recovered from fecal samples) in individual chimpanzees before and during episodes of clinical disease. We restricted our analyses to viruses thought to infect mammals or primarily associated with mammals, discarding viruses associated with nonmammalian hosts. We found 18 viruses (nine of which were previously identified in this population) from at least five viral families. Viral richness (number of viruses per sample) did not vary by health status. By contrast, total viral load (normalized proportion of sequences mapping to viruses) was significantly higher in ill individuals compared with healthy individuals. Furthermore, when ill, Kanyawara chimpanzees exhibited higher viral loads than Ngogo chimpanzees, and males, but not females, exhibited higher infection rates with certain viruses and higher total viral loads as they aged. Post-hoc analyses, including the use of a machine-learning classification method, indicated that one virus, salivirus (Picornaviridae), was the main contributor to health-related and community-level variation in viral loads. Another virus, chimpanzee stool-associated virus (chisavirus; unclassified Picornavirales), was associated with ill health at Ngogo but not at Kanyawara. Chisavirus, chimpanzee adenovirus (Adenoviridae), and bufavirus (Parvoviridae) were also associated with increased age in males. Associations with sex and age are consistent with the hypothesis that nonlethal viral infections cumulatively reflect or contribute to senescence in long-lived species such as chimpanzees.}, }
@article {pmid35014949, year = {2022}, author = {Gaio, D and Anantanawat, K and To, J and Liu, M and Monahan, L and Darling, AE}, title = {Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction.}, journal = {Microbial genomics}, volume = {8}, number = {1}, pages = {}, doi = {10.1099/mgen.0.000744}, pmid = {35014949}, issn = {2057-5858}, abstract = {We developed a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 14 times more libraries for high-throughput Illumina sequencing to be generated for the same cost. We call this new method Hackflex. The quality of library preparation was tested by constructing libraries from Escherichia coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex (recently renamed as Illumina DNA Prep) or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. In order to test the library quality for genomes with a higher and a lower G+C content, library construction methods were also tested on Pseudomonas aeruginosa PAO1 and Staphylococcus aureus ATCC 25923, respectively. We demonstrated that Hackflex can produce high-quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. We show that strongly size-selected libraries produce sufficient yield and complexity to support de novo microbial genome assembly, and that assemblies of the large-insert libraries can be much more contiguous than standard libraries without strong size selection. We introduce a new set of sample barcodes that are distinct from standard Illumina barcodes, enabling Hackflex samples to be multiplexed with samples barcoded using standard Illumina kits. Using Hackflex, we were able to achieve a per-sample reagent cost for library prep of A$7.22 (Australian dollars) (US $5.60; UK £3.87, £1=A$1.87), which is 9.87 times lower than the standard Nextera Flex protocol at advertised retail price. An additional simple modification and further simplification of the protocol by omitting the wash step enables a further price reduction to reach an overall 14-fold cost saving. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programmes where sequencing large numbers of libraries is beneficial.}, }
@article {pmid35014874, year = {2022}, author = {Palomo, A and Dechesne, A and Cordero, OX and Smets, BF}, title = {Evolutionary Ecology of Natural Comammox Nitrospira Populations.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0113921}, doi = {10.1128/msystems.01139-21}, pmid = {35014874}, issn = {2379-5077}, abstract = {Microbes commonly exist in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interaction and evolution has increased during the last decades, but most studies of evolutionary dynamics are based on single species in isolation or in experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filter as a model to avoid this limitation. In these open systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters communities revealed systematic co-occurrence of at least five comammox Nitrospira species, likely promoted by low ammonium concentrations. These Nitrospira species showed intrapopulation sequence diversity, although possible clonal expansion was detected in a few abundant local comammox populations. Nitrospira species showed low homologous recombination and strong purifying selection, the latter process being especially strong in genes essential in energy metabolism. Positive selection was detected for genes related to resistance to foreign DNA and phages. We found that, compared to other habitats, groundwater-fed sand filters impose strong purifying selection and low recombination on comammox Nitrospira populations. These results suggest that evolutionary processes are more affected by habitat type than by species identity. Together, this study improves our understanding of species interaction and evolution in complex microbial communities and sheds light on the environmental dependency of evolutionary processes. IMPORTANCE Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems. In this study, these limitations are circumvented by examining the microbial communities found in stable and well-described groundwater-fed sand filters. Combining metagenomics and strain-level analyses, we identified the microbial interactions and evolutionary processes affecting comammox Nitrospira, a recently discovered bacterial type capable of performing the whole nitrification process. We found that abundant and co-occurrent Nitrospira populations in groundwater-fed sand filters are characterized by low recombination and strong purifying selection. In addition, by comparing these observations with those obtained from Nitrospira species inhabiting other environments, we revealed that evolutionary processes are more affected by habitat type than by species identity.}, }
@article {pmid35014868, year = {2022}, author = {Wu, X and Rensing, C and Han, D and Xiao, KQ and Dai, Y and Tang, Z and Liesack, W and Peng, J and Cui, Z and Zhang, F}, title = {Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0110721}, doi = {10.1128/msystems.01107-21}, pmid = {35014868}, issn = {2379-5077}, abstract = {Enhancing soil phosphate solubilization is a promising strategy for agricultural sustainability, while little is known about the mechanisms of how microorganisms cope with differing phosphorus availability. Using a combination of genome-resolved metagenomics and amplicon sequencing, we investigated the microbial mechanisms involved in phosphorus cycling under three agricultural treatments in a wheat-maize rotation system and two natural reforestation treatments. Available soil phosphorus was the key factor shaping bacterial and fungal community composition and function across our agricultural and reforestation sites. Membrane-bound quinoprotein glucose dehydrogenase (PQQGDH) and exopolyphosphatases (PPX) governed microbial phosphate solubilization in agroecosystems. In contrast, genes encoding glycerol-3-phosphate transporters (ugpB, ugpC, and ugpQ) displayed a significantly greater abundance in the reforestation soils. The gcd gene encoding PQQGDH was found to be the best determinant for bioavailable soil phosphorus. Metagenome-assembled genomes (MAGs) affiliated with Cyclobacteriaceae and Vicinamibacterales were obtained from agricultural soils. Their MAGs harbored not only gcd but also the pit gene encoding low-affinity phosphate transporters. MAGs obtained from reforestation soils were affiliated with Microtrichales and Burkholderiales. These contain ugp genes but no gcd, and thereby are indicative of a phosphate transporter strategy. Our study demonstrates that knowledge of distinct microbial phosphorus acquisition strategies between agricultural and reforestation soils could help in linking microbial processes with phosphorus cycling. IMPORTANCE The soil microbiome is the key player regulating phosphorus cycling processes. Identifying phosphate-solubilizing bacteria and utilizing them for release of recalcitrant phosphate that is bound to rocks or minerals have implications for improving crop nutrient acquisition and crop productivity. In this study, we combined functional metagenomics and amplicon sequencing to analyze microbial phosphorus cycling processes in natural reforestation and agricultural soils. We found that the phosphorus acquisition strategies significantly differed between these two ecosystems. A microbial phosphorus solubilization strategy dominated in the agricultural soils, while a microbial phosphate transporter strategy was observed in the reforestation soils. We further identified microbial taxa that contributed to enhanced phosphate solubilization in the agroecosystem. These microbes are predicted to be beneficial for the increase in phosphate bioavailability through agricultural practices.}, }
@article {pmid35013924, year = {2022}, author = {Bhende, RS and Jhariya, U and Srivastava, S and Bombaywala, S and Das, S and Dafale, NA}, title = {Environmental Distribution, Metabolic Fate, and Degradation Mechanism of Chlorpyrifos: Recent and Future Perspectives.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {35013924}, issn = {1559-0291}, abstract = {Pesticides play a significant role in crop production and have become an inevitable part of the modern environment due to their extensive distribution throughout the soil ecosystem. Prophylactic applications of chlorpyrifos (CP) affect soil fertility, modify soil microbial community structure, and pose potential health risks to the nontarget organisms. Bioremediation through microbial metabolism is found to be an ecofriendly and cheaper process for CP removal from the environment. So far, various bacterial and fungal communities have been reported for CP and its metabolites degradation. Organophosphorus hydrolase (OPH) and methyl parathion hydrolase (MPH) are crucial bacterial enzymes for CP degradation as they efficiently hydrolyze the unbreakable P-O and P = S bond. This review discusses the prospects of toxicity level, persistency, and harmful effects of CP on the environment. CP degradation mechanisms, metabolic pathways, and key enzymes, along with their structural details, are also featured. The highlights on molecular docking with OPH and MPH enzyme for CP show the best binding affinity with OPH; hence, it is an essential part of CP degradation. Simultaneously, metagenomic analysis of soil from contaminated agricultural lands and wastewater was analyzed with the goal to identify the dominant CP degraders and enzymes. The identification of potent degraders, key enzymes, and evaluation of microbial community dynamics upon pesticide exposure can be used as a warning for its dissemination and biomagnification into the food chain.}, }
@article {pmid35013454, year = {2022}, author = {Casimiro-Soriguer, CS and Loucera, C and Peña-Chilet, M and Dopazo, J}, title = {Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {450}, pmid = {35013454}, issn = {2045-2322}, support = {PAIDI2020- DOC_00350//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía/ ; PID2020-117979RB-I00//Ministerio de Ciencia e Innovación/ ; IMP/0019//Instituto de Salud Carlos III/ ; 813533//H2020 Marie Skłodowska-Curie Actions/ ; 676559//H2020 Research Infrastructures/ ; }, abstract = {Gut microbiome is gaining interest because of its links with several diseases, including colorectal cancer (CRC), as well as the possibility of being used to obtain non-intrusive predictive disease biomarkers. Here we performed a meta-analysis of 1042 fecal metagenomic samples from seven publicly available studies. We used an interpretable machine learning approach based on functional profiles, instead of the conventional taxonomic profiles, to produce a highly accurate predictor of CRC with better precision than those of previous proposals. Moreover, this approach is also able to discriminate samples with adenoma, which makes this approach very promising for CRC prevention by detecting early stages in which intervention is easier and more effective. In addition, interpretable machine learning methods allow extracting features relevant for the classification, which reveals basic molecular mechanisms accounting for the changes undergone by the microbiome functional landscape in the transition from healthy gut to adenoma and CRC conditions. Functional profiles have demonstrated superior accuracy in predicting CRC and adenoma conditions than taxonomic profiles and additionally, in a context of explainable machine learning, provide useful hints on the molecular mechanisms operating in the microbiota behind these conditions.}, }
@article {pmid35013392, year = {2022}, author = {Mousavi, SH and Sadeghian Motahar, SS and Salami, M and Kavousi, K and Sheykh Abdollahzadeh Mamaghani, A and Ariaeenejad, S and Salekdeh, GH}, title = {Invitro bioprocessing of corn as poultry feed additive by the influence of carbohydrate hydrolyzing metagenome derived enzyme cocktail.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {405}, pmid = {35013392}, issn = {2045-2322}, abstract = {The carbohydrate-hydrolyzing enzymes play a crucial role in increasing the phenolic content and nutritional properties of polysaccharides substrate, essential for cost-effective industrial applications. Also, improving the feed efficiency of poultry is essential to achieve significant economic benefits. The current study introduced a novel thermostable metagenome-derived xylanase named PersiXyn8 and investigated its synergistic effect with previously reported α-amylase (PersiAmy3) to enhance poultry feed utilization. The potential of the enzyme cocktail in the degradation of poultry feed was analyzed and showed 346.73 mg/g poultry feed reducing sugar after 72 h of hydrolysis. Next, the impact of solid-state fermentation on corn quality was investigated in the presence and absence of enzymes. The phenolic content increased from 36.60 mg/g GAE in control sample to 68.23 mg/g in the presence of enzymes. In addition, the enzyme-treated sample showed the highest reducing power OD 700 of 0.217 and the most potent radical scavenging activity against ABTS (40.36%) and DPPH (45.21%) radicals. Moreover, the protein and ash contents of the fermented corn increased by 4.88% and 6.46%, respectively. These results confirmed the potential of the carbohydrate-hydrolyzing enzymes cocktail as a low-cost treatment for improving the phenolic content, antioxidant activity, and nutritional values of corn for supplementation of corn-based poultry feed.}, }
@article {pmid35013297, year = {2022}, author = {Yan, W and Hall, AB and Jiang, X}, title = {Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {1}, pmid = {35013297}, issn = {2055-5008}, abstract = {Antibiotic-resistance genes (ARGs) regulated by invertible promoters can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of these ARGs regulated by invertible promoters remains poorly understood. Here, we sought to assess the threat posed by ARGs regulated by invertible promoters by systematically searching for ARGs regulated by invertible promoters in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified ARGs regulated by invertible promoters and categorized them into three classes based on the invertase-regulating phase variation. In the human gut microbiome, ARGs regulated by invertible promoters are exclusively found in Bacteroidales species. Through genomic analysis, we observed that ARGs regulated by invertible promoters have convergently originated from ARG insertions into glycan-synthesis loci that were regulated by invertible promoters at least three times. Moreover, all three classes of invertible promoters regulating ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of ARGs regulated by invertible promoters. Overall, these findings reveal that glycan-synthesis loci regulated by invertible promoters in Bacteroidales species are an important hotspot for the emergence of clinically-relevant ARGs regulated by invertible promoters.}, }
@article {pmid35013099, year = {2022}, author = {Zhao, H and Jin, K and Jiang, C and Pan, F and Wu, J and Luan, H and Zhao, Z and Chen, J and Mou, T and Wang, Z and Lu, J and Lu, S and Hu, S and Xu, Y and Huang, M}, title = {A pilot exploration of multi-omics research of gut microbiome in major depressive disorders.}, journal = {Translational psychiatry}, volume = {12}, number = {1}, pages = {8}, pmid = {35013099}, issn = {2158-3188}, support = {No. 81601182//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 81601182//National Natural Science Foundation of China (National Science Foundation of China)/ ; LQ20H090010//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; }, abstract = {The pathophysiology of major depressive disorder (MDD) remains obscure. Recently, the microbiota-gut-brain (MGB) axis's role in MDD has an increasing attention. However, the specific mechanism of the multi-level effects of gut microbiota on host metabolism, immunity, and brain structure is unclear. Multi-omics approaches based on the analysis of different body fluids and tissues using a variety of analytical platforms have the potential to provide a deeper understanding of MGB axis disorders. Therefore, the data of metagenomics, metabolomic, inflammatory factors, and MRI scanning are collected from the two groups including 24 drug-naïve MDD patients and 26 healthy controls (HCs). Then, the correlation analysis is performed in all omics. The results confirmed that there are many markedly altered differences, such as elevated Actinobacteria abundance, plasma IL-1β concentration, lipid, vitamin, and carbohydrate metabolism disorder, and diminished grey matter volume (GMV) of inferior frontal gyrus (IFG) in the MDD patients. Notably, three kinds of discriminative bacteria, Ruminococcus bromii, Lactococcus chungangensis, and Streptococcus gallolyticus have an extensive correlation with metabolome, immunology, GMV, and clinical symptoms. All three microbiota are closely related to IL-1β and lipids (as an example, phosphoethanolamine (PEA)). Besides, Lactococcus chungangensis is negatively related to the GMV of left IFG. Overall, this study demonstrate that the effects of gut microbiome exert in MDD is multifactorial.}, }
@article {pmid35011106, year = {2022}, author = {Pivari, F and Mingione, A and Piazzini, G and Ceccarani, C and Ottaviano, E and Brasacchio, C and Dei Cas, M and Vischi, M and Cozzolino, MG and Fogagnolo, P and Riva, A and Petrangolini, G and Barrea, L and Di Renzo, L and Borghi, E and Signorelli, P and Paroni, R and Soldati, L}, title = {Curcumin Supplementation (Meriva®) Modulates Inflammation, Lipid Peroxidation and Gut Microbiota Composition in Chronic Kidney Disease.}, journal = {Nutrients}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/nu14010231}, pmid = {35011106}, issn = {2072-6643}, abstract = {Chronic kidney disease (CKD) subjects suffer from high risk of cardiovascular mortality, and any intervention preventing the progression of CKD may have an enormous impact on public health. In the last decade, there has been growing awareness that the gut microbiota (GM) can play a pivotal role in controlling the pathogenesis of systemic inflammatory state and CKD progression. To ameliorate the quality of life in CKD subjects, the use of dietary supplements has increased over time. Among those, curcumin has demonstrated significant in vitro anti-inflammatory properties. In this pilot study, 24 CKD patients and 20 healthy volunteers were recruited. CKD patients followed nutritional counselling and were supplemented with curcumin (Meriva®) for six months. Different parameters were evaluated at baseline and after 3-6 months: uremic toxins, metagenomic of GM, and nutritional, inflammatory, and oxidative status. Curcumin significantly reduced plasma pro-inflammatory mediators (CCL-2, IFN-γ, and IL-4) and lipid peroxidation. Regarding GM, after 6 months of curcumin supplementation, Escherichia-Shigella was significantly lower, while Lachnoclostridium was significant higher. Notably, at family level, Lactobacillaceae spp. were found significantly higher in the last 3 months of supplementation. No adverse events were observed in the supplemented group, confirming the good safety profile of curcumin phytosome after long-term administration.}, }
@article {pmid35010887, year = {2021}, author = {Pinart, M and Dötsch, A and Schlicht, K and Laudes, M and Bouwman, J and Forslund, SK and Pischon, T and Nimptsch, K}, title = {Gut Microbiome Composition in Obese and Non-Obese Persons: A Systematic Review and Meta-Analysis.}, journal = {Nutrients}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/nu14010012}, pmid = {35010887}, issn = {2072-6643}, support = {01EA1906B//Federal Ministry of Food and Agriculture/ ; }, abstract = {Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using high-throughput sequencing technologies. We conducted a systematic review in PubMed and Embase including 32 cross-sectional studies assessing the gut microbiome composition by high-throughput sequencing in obese and non-obese adults. A significantly lower alpha diversity (Shannon index) in obese versus non-obese adults was observed in nine out of 22 studies, and meta-analysis of seven studies revealed a non-significant mean difference (-0.06, 95% CI -0.24, 0.12, I2 = 81%). At the phylum level, significantly more Firmicutes and fewer Bacteroidetes in obese versus non-obese adults were observed in six out of seventeen, and in four out of eighteen studies, respectively. Meta-analyses of six studies revealed significantly higher Firmicutes (5.50, 95% 0.27, 10.73, I2 = 81%) and non-significantly lower Bacteroidetes (-4.79, 95% CI -10.77, 1.20, I2 = 86%). At the genus level, lower relative proportions of Bifidobacterium and Eggerthella and higher Acidaminococcus, Anaerococcus, Catenibacterium, Dialister, Dorea, Escherichia-Shigella, Eubacterium, Fusobacterium, Megasphera, Prevotella, Roseburia, Streptococcus, and Sutterella were found in obese versus non-obese adults. Although a proportion of studies found lower diversity and differences in gut microbiome composition in obese versus non-obese adults, the observed heterogeneity across studies precludes clear answers.}, }
@article {pmid35010596, year = {2021}, author = {Jałowiecki, Ł and Hubeny, J and Harnisz, M and Płaza, G}, title = {Seasonal and Technological Shifts of the WHO Priority Multi-Resistant Pathogens in Municipal Wastewater Treatment Plant and Its Receiving Surface Water: A Case Study.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {1}, pages = {}, doi = {10.3390/ijerph19010336}, pmid = {35010596}, issn = {1660-4601}, abstract = {The present study was focused on the identification of multi-resistant bacteria from the WHO priority pathogens list in the samples taken from different stages of the full-scale municipal wastewater treatment plant and receiving water. Additionally, the seasonal variations of the selected multi-resistant pathogens were analyzed in the samples. In order to the aim of the study, the metagenomic DNA from the collected samples was isolated and sequenced. The samples were collected in three campaigns (spring, summer, autumn). Metagenomic DNA was isolated by the commercial kits, according to the manufacturer's instruction. Illumina sequencing system was employed, and the R program was used to metagenomic analysis. It was found that the wastewater samples and receiving water contained the multi-resistant bacteria from the WHO priority pathogens list. The seasonal and technological variations affected the distribution of the pathogens in the wastewater. No effect of the effluent on the pathogens in the receiving water was observed. The results indicated that antibiotic-resistant "priority pathogens" from the WHO list are there in the waste- and receiving water. Technological process and seasons effected their distribution in the environment. Metagenomic analysis can be used as sufficient tool in microbiological and human health risk assessment.}, }
@article {pmid35010187, year = {2021}, author = {Jiang, L and Xian, S and Liu, X and Shen, G and Zhang, Z and Hou, X and Chen, A}, title = {Metagenomic Study on Chinese Homemade Paocai: The Effects of Raw Materials and Fermentation Periods on the Microbial Ecology and Volatile Components.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/foods11010062}, pmid = {35010187}, issn = {2304-8158}, support = {No. 2017YFC0505106-3//Research and Development of Utilization Technology of characteristic Biological Resources in Ar-id Valley of Southwest China/ ; }, abstract = {"Chinese paocai" is typically made by fermenting red radish or cabbage with aged brine (6-8 w/w). This study aimed to reveal the effects of paocai raw materials on fermentation microorganisms by metagenomics sequencing technology, and on volatile organic compounds (VOCs) by gas chromatography-mass spectroscopy, using red radish or cabbage fermented for six rounds with aged brine. The results showed that in the same fermentation period, the microbial diversity in cabbage was higher than that in red radish. Secundilactobacillus paracollinoides and Furfurilactobacillus siliginis were the characteristic bacteria in red radish paocai, whereas 15 species of characteristic microbes were found in cabbage. Thirteen kinds of VOCs were different between the two raw materials and the correlation between the microorganisms and VOCs showed that cabbage paocai had stronger correlations than radish paocai for the most significant relationship between 4-isopropylbenzyl alcohol, α-cadinol, terpinolene and isobutyl phenylacetate. The results of this study provide a theoretical basis for understanding the microbiota and their relation to the characteristic flavors of the fermented paocai.}, }
@article {pmid35008807, year = {2021}, author = {Büchler, AC and Lazarevic, V and Gaïa, N and Girard, M and Eckstein, F and Egli, A and Sutter, ST and Schrenzel, J}, title = {Mycobacterium chelonae Infection Identified by Metagenomic Next-Generation Sequencing as the Probable Cause of Acute Contained Rupture of a Biological Composite Graft-A Case Report.}, journal = {International journal of molecular sciences}, volume = {23}, number = {1}, pages = {}, doi = {10.3390/ijms23010381}, pmid = {35008807}, issn = {1422-0067}, abstract = {We present the case of a 72-year-old female patient with acute contained rupture of a biological composite graft, 21 months after replacement of the aortic valve and the ascending aorta due to an aortic dissection. Auramine-rhodamine staining of intraoperative biopsies showed acid-fast bacilli, but classical culture and molecular methods failed to identify any organism. Metagenomic analysis indicated infection with Mycobacterium&amp;nbsp;chelonae, which was confirmed by target-specific qPCR. The complexity of the sample required a customized bioinformatics pipeline, including cleaning steps to remove sequences of human, bovine ad pig origin. Our study underlines the importance of multiple testing to increase the likelihood of pathogen identification in highly complex samples.}, }
@article {pmid34730826, year = {2022}, author = {Chen, H and Chu, JS and Chen, J and Luo, Q and Wang, H and Lu, R and Zhu, Z and Yuan, G and Yi, X and Mao, Y and Lu, C and Wang, Z and Gu, D and Jin, Z and Zhang, C and Weng, Z and Li, S and Yan, X and Yang, R}, title = {Insights into the Ancient Adaptation to Intertidal Environments by Red Algae Based on a Genomic and Multiomics Investigation of Neoporphyra haitanensis.}, journal = {Molecular biology and evolution}, volume = {39}, number = {1}, pages = {}, doi = {10.1093/molbev/msab315}, pmid = {34730826}, issn = {1537-1719}, abstract = {Colonization of land from marine environments was a major transition for biological life on Earth, and intertidal adaptation was a key evolutionary event in the transition from marine- to land-based lifestyles. Multicellular intertidal red algae exhibit the earliest, systematic, and successful adaptation to intertidal environments, with Porphyra sensu lato (Bangiales, Rhodophyta) being a typical example. Here, a chromosome-level 49.67 Mb genome for Neoporphyra haitanensis comprising 9,496 gene loci is described based on metagenome-Hi-C-assisted whole-genome assembly, which allowed the isolation of epiphytic bacterial genome sequences from a seaweed genome for the first time. The compact, function-rich N. haitanensis genome revealed that ancestral lineages of red algae share common horizontal gene transfer events and close relationships with epiphytic bacterial populations. Specifically, the ancestor of N. haitanensis obtained unique lipoxygenase family genes from bacteria for complex chemical defense, carbonic anhydrases for survival in shell-borne conchocelis lifestyle stages, and numerous genes involved in stress tolerance. Combined proteomic, transcriptomic, and metabolomic analyses revealed complex regulation of rapid responses to intertidal dehydration/rehydration cycling within N. haitanensis. These adaptations include rapid regulation of its photosynthetic system, a readily available capacity to utilize ribosomal stores, increased methylation activity to rapidly synthesize proteins, and a strong anti-oxidation system to dissipate excess redox energy upon exposure to air. These novel insights into the unique adaptations of red algae to intertidal lifestyles inform our understanding of adaptations to intertidal ecosystems and the unique evolutionary steps required for intertidal colonization by biological life.}, }
@article {pmid34705550, year = {2022}, author = {Carroll, J and Van Oostende, N and Ward, BB}, title = {Evaluation of Genomic Sequence-Based Growth Rate Methods for Synchronized Synechococcus Cultures.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {1}, pages = {e0174321}, doi = {10.1128/AEM.01743-21}, pmid = {34705550}, issn = {1098-5336}, support = {1747511//National Science Foundation (NSF)/ ; }, abstract = {Standard methods for calculating microbial growth rates (μ) through the use of proxies, such as in situ fluorescence, cell cycle, or cell counts, are critical for determining the magnitude of the role bacteria play in marine carbon (C) and nitrogen (N) cycles. Taxon-specific growth rates in mixed assemblages would be useful for attributing biogeochemical processes to individual species and understanding niche differentiation among related clades, such as found in Synechococcus and Prochlorococcus. We tested three novel DNA sequencing-based methods (iRep, bPTR, and GRiD) for evaluating the growth of light-synchronized Synechococcus cultures under different light intensities and temperatures. In vivo fluorescence and cell cycle analysis were used to obtain standard estimates of growth rate for comparison with those of the sequence-based methods (SBM). None of the SBM values were correlated with growth rates calculated by standard techniques despite the fact that all three SBM were correlated with the percentage of cells in S phase (DNA replication) over the diel cycle. Inaccuracy in determining the time of maximum DNA replication is unlikely to account entirely for the absence of a relationship between SBM and growth rate, but the fact that most microbes in the surface ocean exhibit some degree of diel cyclicity is a caution for application of these methods. SBM correlate with DNA replication but cannot be interpreted quantitatively in terms of growth rate. IMPORTANCE Small but abundant, cyanobacterial strains such as the photosynthetic Synechococcus spp. are important because they contribute significantly to primary productivity in the ocean. These bacteria generate oxygen and provide biologically available carbon, which is essential for organisms at higher trophic levels. The small size and diversity of natural microbial assemblages mean that taxon-specific activities (e.g., growth rate) are difficult to obtain in the field. It has been suggested that sequence-based methods (SBM) may be able to solve this problem. We find, however, that SBM can detect DNA replication and are correlated with phases of the cell cycle but cannot be interpreted in terms of absolute growth rate for Synechococcus cultures growing under a day-night cycle, like that experienced in the ocean.}, }
@article {pmid34301806, year = {2021}, author = {Xie, Y and Song, L and Yang, J and Tao, T and Yu, J and Shi, J and Jin, X}, title = {Small intestinal flora graft alters fecal flora, stool, cytokines and mood status in healthy mice.}, journal = {Life science alliance}, volume = {4}, number = {9}, pages = {}, pmid = {34301806}, issn = {2575-1077}, mesh = {*Affect ; Animals ; *Behavior, Animal ; Biomarkers ; Body Weight ; Cytokines/blood/*metabolism ; Drinking ; Eating ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Male ; Metagenome ; Metagenomics ; Mice ; }, abstract = {Fecal microbiota transplantation is widely used. Large intestinal microbiota (LIM) is more similar to fecal microbiota than small intestinal microbiota (SIM). The SIM communities are very different from those of LIM. Therefore, SIM transplantation (SIMT) and LIM transplantation (LIMT) might exert different influences. Here, healthy adult male C57Bl/6 mice received intragastric SIMT, LIMT, or sterile PBS administration. Microbiota graft samples were collected from small/large intestine of healthy mice of the same age, sex, and strain background. Compared with PBS treatment, SIMT increased pellet number, stool wet weight, and stool water percentage; induced a fecal microbiota profile shift toward the microbial composition of the SIM graft; induced a systemic anti-inflammatory cytokines profile; and ameliorated depressive-like behaviors in recipients. LIMT, however, induced merely a slight alteration in fecal microbial composition and no significant influence on the other aspects. In sum, SIMT, rather than LIMT, affected defecation features, fecal microbial composition, cytokines profile, and depressive-like behaviors in healthy mice. This study reveals the different effects of SIMT and LIMT, providing an interesting clue for further researches involving gut microbial composition change.}, }
@article {pmid33845884, year = {2021}, author = {Garg, S}, title = {Computational methods for chromosome-scale haplotype reconstruction.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {101}, pmid = {33845884}, issn = {1474-760X}, mesh = {*Chromosomes ; Computational Biology/*methods ; Diploidy ; Genomics/*methods ; *Haplotypes ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; Polyploidy ; Sequence Analysis, DNA/methods ; }, abstract = {High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent and discuss methodological progress and perspectives in these areas.}, }
@article {pmid33726811, year = {2021}, author = {Yi, H and Lin, Y and Lin, C and Jin, W}, title = {Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {84}, pmid = {33726811}, issn = {1474-760X}, mesh = {Algorithms ; Bacteria/genetics ; Computational Biology/*methods/standards ; Databases, Genetic ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods/standards ; Sequence Analysis, DNA ; *Software ; }, abstract = {Here, we develop k -mer substring space decomposition (Kssd), a sketching technique which is significantly faster and more accurate than current sketching methods. We show that it is the only method that can be used for large-scale dataset comparisons at population resolution on simulated and real data. Using Kssd, we prioritize references for all 1,019,179 bacteria whole genome sequencing (WGS) runs from NCBI Sequence Read Archive and find misidentification or contamination in 6164 of these. Additionally, we analyze WGS and exome runs of samples from the 1000 Genomes Project.}, }
@article {pmid35008051, year = {2022}, author = {Anderson, J and Fish, D and Armstrong, P and Misencik, M and Bransfield, A and Ferrandino, F and Andreadis, T and Stenglein, M and Kapuscinski, M}, title = {Seasonal Dynamics of Mosquito-Borne Viruses in the Southwestern Florida Everglades, 2016, 2017.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.20-1547}, pmid = {35008051}, issn = {1476-1645}, abstract = {Mosquitoes were collected for 12 consecutive months beginning June 2016, from 11 locations in the Florida Everglades, Collier County, and tested for viruses by isolation in Vero cells and subsequent identification. One species complex and 31 species of mosquitoes were identified from 668,809 specimens. Ochlerotatus taeniorhynchus comprised 72.2% of the collection. Other notable species were Anopheles crucians complex, Culex nigripalpus, Cx. erraticus, and Cx. cedecei. Seven species of virus were identified from 110 isolations: Everglades, Gumbo Limbo, Mahogany Hammock, Pahayokee, Shark River, Tensaw, and West Nile viruses. Everglades, West Nile, Tensaw, and Mahogany Hammock viruses were most frequently isolated. Largest numbers of viruses were identified from Cx. cedecei, Cx. nigripalpus, and An. crucians complex. Five species of virus were isolated from Cx. cedecei. Viruses were isolated from mangrove, cypress swamp, hardwood hammock, and sawgrass habitats. West Nile virus was isolated August through October when Cx. nigripalpus was most abundant. Everglades virus was the most frequently isolated virus from nine species of mosquitoes collected from June through August. Tensaw virus was isolated primarily from Anopheles species. Isolations were made in July, August, January, February, and April, suggesting that this virus may be present in host-seeking mosquitoes throughout the year. Mahogany Hammock, Shark River, Gumbo Limbo, and Pahayokee viruses were isolated primarily from Cx. cedecei from June through December. Shotgun metagenomic sequencing was used to document that seven pools of Cx. cedecei were infected with two arboviruses. As communities expand into the Everglades, more humans will become exposed to arboviruses.}, }
@article {pmid35007432, year = {2021}, author = {Ibrahim, A and Maatouk, M and Rajaonison, A and Zgheib, R and Haddad, G and Bou Khalil, J and Raoult, D and Bittar, F}, title = {Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation.}, journal = {Microbiology spectrum}, volume = {9}, number = {3}, pages = {e0106921}, doi = {10.1128/spectrum.01069-21}, pmid = {35007432}, issn = {2165-0497}, support = {10-IAHU-03//Agence Nationale de la Recherche (ANR)/ ; }, abstract = {The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, the candidate phyla radiation (CPR) group has been recognized as representing a large proportion of the microbial kingdom (>26%). CPR are characterized by their obligate symbiotic or exoparasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the coculture of CPR with a suitable bacterial host. Based on various sputum samples, we tried to enrich CPR (Saccharibacteria members) and to cocultivate them with pure hosts (Schaalia odontolytica). This protocol was monitored by TaqMan real-time quantitative PCR (qPCR) using a system specific for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in coculturing and sequencing the complete genomes of two new Saccharibacteria species, "Candidatus Minimicrobia naudis" and "Candidatus Minimicrobia vallesae." In addition, we noticed a decrease in the CT values of Saccharibacteria and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members, and in the future, their currently unknown characteristics may be revealed. IMPORTANCE In this study, the first TaqMan real-time quantitative PCR (qPCR) system, targeting Saccharibacteria phylum, has been developed. This technique can specifically quantify Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific, and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol facilitates subsequent studies of the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database.}, }
@article {pmid35006678, year = {2022}, author = {Li, Y and Guo, L and Häggblom, MM and Yang, R and Li, M and Sun, X and Chen, Z and Li, F and Su, X and Yan, G and Xiao, E and Zhang, H and Sun, W}, title = {Serratia spp. Are Responsible for Nitrogen Fixation Fueled by As(III) Oxidation, a Novel Biogeochemical Process Identified in Mine Tailings.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.1c06857}, pmid = {35006678}, issn = {1520-5851}, abstract = {Biological nitrogen fixation (BNF) has important environmental implications in tailings by providing bioavailable nitrogen to these habitats and sustaining ecosystem functions. Previously, chemolithotrophic diazotrophs that dominate in mine tailings were shown to use reduced sulfur (S) as the electron donor. Tailings often contain high concentrations of As(III) that might function as an alternative electron donor to fuel BNF. Here, we tested this hypothesis and report on BNF fueled by As(III) oxidation as a novel biogeochemical process in addition to BNF fueled by S. Arsenic (As)-dependent BNF was detected in cultures inoculated from As-rich tailing samples derived from the Xikuangshan mining area in China, as suggested by nitrogenase activity assays, quantitative polymerase chain reaction, and 15N2 enrichment incubations. As-dependent BNF was also active in eight other As-contaminated tailings and soils, suggesting that the potential for As-dependent BNF may be widespread in As-rich habitats. DNA-stable isotope probing identified Serratia spp. as the bacteria responsible for As-dependent BNF. Metagenomic binning indicated that the essential genes for As-dependent BNF [i.e., nitrogen fixation, As(III) oxidation, and carbon fixation] were present in Serratia-associated metagenome-assembled genomes. Over 20 Serratia genomes obtained from NCBI also contained essential genes for both As(III) oxidation and BNF (i.e., aioA and nifH), suggesting that As-dependent BNF may be a widespread metabolic trait in Serratia spp.}, }
@article {pmid35005906, year = {2022}, author = {Tang, Y and Sun, J and Dong, B and Dai, X}, title = {Thermal Hydrolysis Pretreatment-Anaerobic Digestion Promotes Plant-Growth Biostimulants Production from Sewage Sludge by Upregulating Aromatic Amino Acids Transformation and Quinones Supply.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.1c06506}, pmid = {35005906}, issn = {1520-5851}, abstract = {Micromolecular plant-growth biostimulants (micro-PBs) production from sewage sludge is attracting increasing interest, as it is expected to enhance the fertilizing effect of sludge for land application. This study attempted to promote effective micro-PBs production from sewage sludge through thermal hydrolysis pretreatment-anaerobic digestion (THP-AD) and explore the underpinning regulation mechanisms. Results showed that the highest effective micro-PB production in digested sludge was achieved in THP(160 °C)-AD by day 12, with 80.73 mg/kg volatile solid (VS) of phytohormones and 417.75 mg/kg VS of allelochemicals, and these effective micro-PBs all originated from aromatic amino acids (AAAs). The metabolomic and metagenomic results revealed that, as compared with THP(120 °C)-AD and AD without THP, THP(160°C)-AD uniquely upregulated AAAs biosynthesis and consequently improved AAAs metabolism toward effective micro-PBs production. Further exploration of related microbial pathways and metabolites suggested that the upregulated AAAs biosynthesis in THP(160 °C)-AD in the early stage was partially attributed to the enhanced carbohydrate release. More importantly, the results showed that the amount of quinones, which probably facilitate energy generation via acting as electron-transfer mediators, was significantly positively correlated with the abundance of AAAs biosynthesis genes (R2 = 0.93). Hence, the improved initial release and biosynthesis of quinones are critical in enhancing the AAAs biosynthesis in THP(160 °C)-AD. Moreover, the enhanced quinones supply and the consequent active AAAs transformation in THP(160 °C)-AD reinforced the humification process, highly supporting effective micro-PBs stabilization. The important roles of quinones in effective micro-PBs production and stabilization in sludge anaerobic digestion should be considered in technology development for micro-PBs recovery.}, }
@article {pmid35004734, year = {2021}, author = {Gao, H and Li, T and Feng, L and Zhang, S}, title = {Elizabethkingia miricola Causes Intracranial Infection: A Case Study.}, journal = {Frontiers in medicine}, volume = {8}, number = {}, pages = {761924}, doi = {10.3389/fmed.2021.761924}, pmid = {35004734}, issn = {2296-858X}, abstract = {Background: Elizabethkingia miricola is a rarely encountered bacterium in clinical practice. It is a rare gram-negative rod-shaped bacterium associated with lung and urinary tract infections, but never found in cerebrospinal fluid. This paper reports a case of an adult patient infected by E. miricola via an unknown route of infection causing a severe intracranial infection. Elizabethkingia miricola was detected by culture and Metagenomic next generation sequencing in CSF. Early identification of this strain and treatment with sensitive antibiotics is necessary to reduce morbidity and mortality. Case Report: A 24-year-old male was admitted to a West China Hospital because of headache and vomiting for 2 months. Symptom features included acute onset and long duration of illness. Notably, headache and vomiting were the primary neurological symptoms. Routine cerebrospinal fluid culture failed to identify the bacterium; however, Elizabethkingia miricola bacterium was detected via second-generation sequencing techniques. Elizabethkingia miricola was found to be a multi-drug resistant organism, hence, treatment with ceftriaxone, a commonly used drug for intracranial infections was ineffective. This strain eventually caused severe intracranial infection resulting in the death of the patient. Conclusion: In summary, this study comprehensively describes a case of an adult patient infected by E. miricola and discusses its early identification as well as application of sensitive antibiotics in the emergency setting.}, }
@article {pmid35004733, year = {2021}, author = {Yi, J and Wang, N and Wu, J and Tang, Y and Zhang, J and Zhu, L and Rui, X and Guo, Y and Xu, Y}, title = {Development of a Droplet Digital Polymerase Chain Reaction for Sensitive Detection of Pneumocystis jirovecii in Respiratory Tract Specimens.}, journal = {Frontiers in medicine}, volume = {8}, number = {}, pages = {761788}, doi = {10.3389/fmed.2021.761788}, pmid = {35004733}, issn = {2296-858X}, abstract = {Background: Pneumocystis jirovecii is a human-specific opportunistic fungus that causes Pneumocystis pneumonia (PCP), a life-threatening opportunistic lung infection that affects immunocompromised patients. P. jirovecii colonization may be linked to the transmission of the infection. The detection of P. jirovecii in immunocompromised patients is thus especially important. The low fungal load and the presence of PCR inhibitors limit the usefulness of quantitative PCR (qPCR) for accurate absolute quantification of P. jirovecii in specimens. Droplet digital PCR (ddPCR), however, presents a methodology that allows higher sensitivity and accuracy. Here, we developed a ddPCR method for detecting P. jirovecii DNA in respiratory specimens, and evaluated its sensitivity against qPCR. Materials and Methods: One bronchoalveolar fluid (BALF) sample each was collected from 82 patients with potential PCP to test the presence of P. jirovecii DNA using both ddPCR and qPCR, and samples with inconsistent results between the two methods were further tested by metagenomic next generation sequencing (mNGS). In addition, 37 sputum samples from 16 patients diagnosed with PCP, as well as continuous respiratory tract specimens from nine patients with PCP and treated with sulfonamides, were also collected for P. jirovecii DNA testing using both ddPCR and qPCR. Results: ddPCR and qPCR gave the same results for 95.12% (78/82) of the BALF samples. The remaining four specimens tested positive using ddPCR but negative using qPCR, and they were found to be positive by mNGS. Detection results of 78.37% (29/37) sputum samples were consistent between ddPCR and qPCR, while the other eight samples tested positive using ddPCR but negative using qPCR. The P. jirovecii load of patients with PCP decreased to undetectable levels after treatment according to qPCR, but P. jirovecii was still detectable using ddPCR. Conclusions: ddPCR was more sensitive than qPCR, especially at detecting low-pathogen-load P. jirovecii. Thus, ddPCR represents a useful, viable, and reliable alternative to qPCR in P. jirovecii testing in patients with immunodeficiency.}, }
@article {pmid35004723, year = {2021}, author = {Liu, K and Gao, Y and Han, J and Han, X and Shi, Y and Liu, C and Li, J}, title = {Diffuse Large B-Cell Lymphoma of the Mandible Diagnosed by Metagenomic Sequencing: A Case Report.}, journal = {Frontiers in medicine}, volume = {8}, number = {}, pages = {752523}, doi = {10.3389/fmed.2021.752523}, pmid = {35004723}, issn = {2296-858X}, abstract = {Introduction: Non-Hodgkin lymphoma (NHL) has a much higher incidence rate than Hodgkin lymphoma. Approximately 40% NHL occurs in extranodal tissues or organs, and its clinical manifestations are often nonspecific. Primary bone NHL involving the mandible is an uncommon NHL that is characterized by fever, gum swelling and toothache. Therefore, it is often misdiagnosed as oral diseases. Case Presentation: A 52-year-old female had recurrent fever for more than 1 month, with numbness in her left jaw and toothache. PET/CT showed an uptake area in the left mandible, suggesting microbial infections. However, antibacterial, and antiviral treatment were ineffective. Furthermore, metagenomic sequencing of plasma reported no pathogens, but instead showed significant copy number variations of multiple chromosomes, which highly suggested the existence of tumor. Finally, diffuse large B-cell lymphoma (DLBCL) was diagnosed by mandibular biopsy, and the patient was transferred to Hematology department for chemotherapy. Conclusion: mNGS not only assists rapid etiological diagnosis, but also helps rule out infection and diagnose malignant neoplasm.}, }
@article {pmid35004620, year = {2021}, author = {Avalon, NE and Murray, AE and Daligault, HE and Lo, CC and Davenport, KW and Dichosa, AEK and Chain, PSG and Baker, BJ}, title = {Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian.}, journal = {Frontiers in chemistry}, volume = {9}, number = {}, pages = {802574}, doi = {10.3389/fchem.2021.802574}, pmid = {35004620}, issn = {2296-2646}, abstract = {Complex interactions exist between microbiomes and their hosts. Increasingly, defensive metabolites that have been attributed to host biosynthetic capability are now being recognized as products of host-associated microbes. These unique metabolites often have bioactivity targets in human disease and can be purposed as pharmaceuticals. Polyketides are a complex family of natural products that often serve as defensive metabolites for competitive or pro-survival purposes for the producing organism, while demonstrating bioactivity in human diseases as cholesterol lowering agents, anti-infectives, and anti-tumor agents. Marine invertebrates and microbes are a rich source of polyketides. Palmerolide A, a polyketide isolated from the Antarctic ascidian Synoicum adareanum, is a vacuolar-ATPase inhibitor with potent bioactivity against melanoma cell lines. The biosynthetic gene clusters (BGCs) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A candidate palmerolide BGC was identified from a S. adareanum microbiome-metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, active site and motif identification were used to identify and propose the function of the ∼75 kbp trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the stepwise synthesis of palmerolide A. Though PKS systems often act in a predictable co-linear sequence, this BGC includes multiple trans-acting enzymatic domains, a non-canonical condensation termination domain, a bacterial luciferase-like monooxygenase (LLM), and is found in multiple copies within the metagenome-assembled genome (MAG). Detailed inspection of the five highly similar pal BGC copies suggests the potential for biosynthesis of other members of the palmerolide chemical family. This is the first delineation of a biosynthetic gene cluster from an Antarctic microbial species, recently proposed as Candidatus Synoicihabitans palmerolidicus. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression.}, }
@article {pmid35004353, year = {2021}, author = {Liu, L and Yuan, M and Shi, Y and Su, X}, title = {Clinical Performance of BAL Metagenomic Next-Generation Sequence and Serum (1,3)-β-D-Glucan for Differential Diagnosis of Pneumocystis jirovecii Pneumonia and Pneumocystis jirovecii Colonisation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {784236}, doi = {10.3389/fcimb.2021.784236}, pmid = {35004353}, issn = {2235-2988}, abstract = {Background: Differentiating Pneumocystis jirovecii infection from colonisation is crucial for appropriate therapy administration. In this study, we evaluated the performance of bronchoalveolar lavage fluid (BAL) metagenomic next-generation sequencing (mNGS) and serum 1,3-β-D-glucan (BDG) tests in differentiating colonisation and infection with P. jirovecii.<br><br>Methods: From January 2018 to March 2021, 47 patients were enrolled in this study at the Hunan Provincial People's Hospital. The final diagnosis was used as a reference, and cases were classified into the P. jirovecii pneumonia (PJP) group or the P. jirovecii colonisation (PJC) group. Clinical data were recorded. The performances of mNGS and BDG were compared.<br><br>Result: The fungal load significantly differed between patients with PJP and PJC, with median reads of 3,215.79 ± 1,797 vs. 5.61 ± 0.88 in the PJP and PJC groups, respectively (P < 0.0001). BDG also significantly differed between the two groups, with a median titre of 233.60 ± 39.65 pg/ml in the PJP group and 68.48 ± 19.21 pg/ml in the PJC group (P = 0.0006). The area under the curve was 0.973 (95%CI: 0.868-1.007) for mNGS of the BAL and 0.879 (95%CI: 0.769-0.989) for the serum BDG. The optimal threshold value for discriminating P. jirovecii infection from colonisation appeared to be 14 reads (sensitivity, 83.3%; specificity, 95.7%; positive likelihood ratio, 19.2) and BDG = 88.6 pg/ml (sensitivity, 79.2%; specificity, 92.9%; positive likelihood ratio, 18.2). No correlation between mNGS reads and the BDG titre was found in mNGS-positive patients (r 2 = 0.0076, P = 0.583). The levels of lactate dehydrogenase and C-reactive protein were significantly higher in the PJP group than in the PJC group.<br><br>Conclusion: BAL mNGS and serum BDG are useful adjunct tests that can assist with differentiating between colonisation and infection of P. jirovecii.}, }
@article {pmid35004342, year = {2021}, author = {Wirth, R and Pap, B and Maróti, G and Vályi, P and Komlósi, L and Barta, N and Strang, O and Minárovits, J and Kovács, KL}, title = {Toward Personalized Oral Diagnosis: Distinct Microbiome Clusters in Periodontitis Biofilms.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {747814}, doi = {10.3389/fcimb.2021.747814}, pmid = {35004342}, issn = {2235-2988}, abstract = {Periodontitis is caused by pathogenic subgingival microbial biofilm development and dysbiotic interactions between host and hosted microbes. A thorough characterization of the subgingival biofilms by deep amplicon sequencing of 121 individual periodontitis pockets of nine patients and whole metagenomic analysis of the saliva microbial community of the same subjects were carried out. Two biofilm sampling methods yielded similar microbial compositions. Taxonomic mapping of all biofilms revealed three distinct microbial clusters. Two clinical diagnostic parameters, probing pocket depth (PPD) and clinical attachment level (CAL), correlated with the cluster mapping. The dysbiotic microbiomes were less diverse than the apparently healthy ones of the same subjects. The most abundant periodontal pathogens were also present in the saliva, although in different representations. The single abundant species Tannerella forsythia was found in the diseased pockets in about 16-17-fold in excess relative to the clinically healthy sulcus, making it suitable as an indicator of periodontitis biofilms. The discrete microbial communities indicate strong selection by the host immune system and allow the design of targeted antibiotic treatment selective against the main periodontal pathogen(s) in the individual patients.}, }
@article {pmid35003022, year = {2021}, author = {Raj, A and Kumar, A and Dames, JF}, title = {Tapping the Role of Microbial Biosurfactants in Pesticide Remediation: An Eco-Friendly Approach for Environmental Sustainability.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {791723}, doi = {10.3389/fmicb.2021.791723}, pmid = {35003022}, issn = {1664-302X}, abstract = {Pesticides are used indiscriminately all over the world to protect crops from pests and pathogens. If they are used in excess, they contaminate the soil and water bodies and negatively affect human health and the environment. However, bioremediation is the most viable option to deal with these pollutants, but it has certain limitations. Therefore, harnessing the role of microbial biosurfactants in pesticide remediation is a promising approach. Biosurfactants are the amphiphilic compounds that can help to increase the bioavailability of pesticides, and speeds up the bioremediation process. Biosurfactants lower the surface area and interfacial tension of immiscible fluids and boost the solubility and sorption of hydrophobic pesticide contaminants. They have the property of biodegradability, low toxicity, high selectivity, and broad action spectrum under extreme pH, temperature, and salinity conditions, as well as a low critical micelle concentration (CMC). All these factors can augment the process of pesticide remediation. Application of metagenomic and in-silico tools would help by rapidly characterizing pesticide degrading microorganisms at a taxonomic and functional level. A comprehensive review of the literature shows that the role of biosurfactants in the biological remediation of pesticides has received limited attention. Therefore, this article is intended to provide a detailed overview of the role of various biosurfactants in improving pesticide remediation as well as different methods used for the detection of microbial biosurfactants. Additionally, this article covers the role of advanced metagenomics tools in characterizing the biosurfactant producing pesticide degrading microbes from different environments.}, }
@article {pmid35003020, year = {2021}, author = {Xing, XW and Yu, SF and Zhang, JT and Tan, RS and Ma, YB and Tian, X and Wang, RF and Yao, GE and Cui, F and Gui, QP and Yu, SY}, title = {Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Cerebral Aspergillosis.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {787863}, doi = {10.3389/fmicb.2021.787863}, pmid = {35003020}, issn = {1664-302X}, abstract = {Purpose: Cerebral aspergillosis (CA) is a rare but often fatal, difficult-to-diagnose, opportunistic infection. The utility of metagenomic next-generation sequencing (mNGS) for diagnosis of CA is unclear. We evaluated the usefulness of mNGS of the cerebrospinal fluid (CSF) for the diagnosis of CA. Methods: This prospective study involved seven consecutive patients with confirmed CA in whom CSF mNGS was performed. Serum (1→3)-β-D-glucan and galactomannan levels were determined, and histopathological examination and mNGS of the CSF were conducted. CSF specimens from three non-infected patients were used as positive controls. Results: mNGS of the CSF was positive in six of the seven confirmed CA cases (85.71% sensitivity). In the cryptococcal meningitis group (control), mNGS of the CSF was positive for Aspergillus in two patients (84.62% specificity). The positive likelihood ratio, negative likelihood ratio, and Youden's index of mNGS for CA in the CSF were 5.565, 0.169, and 0.7, respectively. Among the six mNGS-positive cases, more than two Aspergillus species were found in four (4/6, 66.67%). In the positive controls, the addition of one A. fumigatus spore yielded a standardised species-specific read number (SDSSRN) of 25.45 by mNGS; the detection rate would be 0.98 if SDSSRN was 2. Conclusion: mNGS facilitates the diagnosis of CA and may reduce the need for cerebral biopsy in patients with suspected CA. Trial Registration Number: Chinese Clinical Trial Registry, ChiCTR1800020442.}, }
@article {pmid35003015, year = {2021}, author = {Sajid, M and Srivastava, S and Kumar, A and Kumar, A and Singh, H and Bharadwaj, M}, title = {Bacteriome of Moist Smokeless Tobacco Products Consumed in India With Emphasis on the Predictive Functional Potential.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {784841}, doi = {10.3389/fmicb.2021.784841}, pmid = {35003015}, issn = {1664-302X}, abstract = {Smokeless tobacco products (STPs) carry assorted microbial population that contributes to carcinogens synthesis like tobacco-specific nitrosamines (TSNAs). Extensive exploration of microbiota-harboring STPs is required to understand their full carcinogenic potential. Here, we applied 16S rRNA gene sequencing to investigate bacteriome present in moist STPs immensely consumed in India (Khaini, Moist-snuff, Qiwam, and Snus). Further, the functional metagenome was speculated by PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) to assign the abundance of genes related to nitrogen metabolism, bacterial toxins, antibiotic drug resistance and other pro-inflammatory molecules. Highly diverse bacterial communities were observed in all moist STPs. Taxonomic analysis revealed a total of 549 genera belonging to four major phyla Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria. Overall, the core bacterial genera Acinetobacter, Bacillus, Prevotella, Acetobacter, Lactobacillus, Paracoccus, Flavobacterium, and Bacteroides were significantly abundant in moist STPs. Elevated moisture-holding products like Moist-snuff and Qiwam harbor rich bacterial species diversity and showed similar bacteriome composition. Furthermore, Qiwam products showed the highest level of genes associated with nitrogen metabolism, antibiotic resistance, toxins, and pro-inflammation (predicted by PICRUSt) which can contribute to the synthesis of TSNAs and induction of oral cancer. The present broad investigation of moist STPs-associated bacteriome prevalence and their detailed metabolic potential will provide novel insight into the oral carcinogenesis induced by STPs.}, }
@article {pmid35003014, year = {2021}, author = {López-González, JA and Estrella-González, MJ and Lerma-Moliz, R and Jurado, MM and Suárez-Estrella, F and López, MJ}, title = {Industrial Composting of Sewage Sludge: Study of the Bacteriome, Sanitation, and Antibiotic-Resistant Strains.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {784071}, doi = {10.3389/fmicb.2021.784071}, pmid = {35003014}, issn = {1664-302X}, abstract = {Wastewater treatment generates a huge amount of sewage sludge, which is a source of environmental pollution. Among the alternatives for the management of this waste, industrial composting stands out as one of the most relevant. The objective of this study was to analyze the bacterial population linked to this process and to determine its effectiveness for the reduction, and even elimination, of microorganisms and pathogens present in these organic wastes. For this purpose, the bacteriome and the fecal bacteria contamination of samples from different sewage sludge industrial composting facilities were evaluated. In addition, fecal bacteria indicators and pathogens, such as Salmonella, were isolated from samples collected at key stages of the process and characterized for antibiotic resistance to macrolide, β-lactam, quinolone, and aminoglycoside families. 16S rRNA phylogeny data revealed that the process clearly evolved toward a prevalence of Firmicutes and Actinobacteria phyla, removing the fecal load. Moreover, antibiotic-resistant microorganisms present in the raw materials were reduced, since these were isolated only in the bio-oxidative phase. Therefore, industrial composting of sewage sludge results in a bio-safe final product suitable for use in a variety of applications.}, }
@article {pmid35002754, year = {2021}, author = {Fernández, J and Fernández-Sanjurjo, M and Iglesias-Gutiérrez, E and Martínez-Camblor, P and Villar, CJ and Tomás-Zapico, C and Fernández-García, B and Lombó, F}, title = {Resistance and Endurance Exercise Training Induce Differential Changes in Gut Microbiota Composition in Murine Models.}, journal = {Frontiers in physiology}, volume = {12}, number = {}, pages = {748854}, doi = {10.3389/fphys.2021.748854}, pmid = {35002754}, issn = {1664-042X}, abstract = {Background: The effect of resistance training on gut microbiota composition has not been explored, despite the evidence about endurance exercise. The aim of this study was to compare the effect of resistance and endurance training on gut microbiota composition in mice. Methods: Cecal samples were collected from 26 C57BL/6N mice, divided into three groups: sedentary (CTL), endurance training on a treadmill (END), and resistance training on a vertical ladder (RES). After 2 weeks of adaption, mice were trained for 4 weeks, 5 days/week. Maximal endurance and resistance capacity test were performed before and after training. Genomic DNA was extracted and 16S Ribosomal RNA sequenced for metagenomics analysis. The percentages for each phylum, class, order, family, or genus/species were obtained using an open-source bioinformatics pipeline. Results: END showed higher diversity and evenness. Significant differences among groups in microbiota composition were only observed at genera and species level. END showed a significantly higher relative abundance of Desulfovibrio and Desulfovibrio sp., while Clostridium and C. cocleatum where higher for RES. Trained mice showed significantly lower relative abundance of Ruminococcus gnavus and higher of the genus Parabacteroides compared to CTL. We explored the relationship between relative taxa abundance and maximal endurance and resistance capacities after the training period. Lachnospiraceae and Lactobacillaceae families were negatively associated with endurance performance, while several taxa, including Prevotellaceae family, Prevotella genus, and Akkermansia muciniphila, were positively correlated. About resistance performance, Desulfovibrio sp. was negatively correlated, while Alistipes showed a positive correlation. Conclusion: Resistance and endurance training differentially modify gut microbiota composition in mice, under a high-controlled environment. Interestingly, taxa associated with anti- and proinflammatory responses presented the same pattern after both models of exercise. Furthermore, the abundance of several taxa was differently related to maximal endurance or resistance performance, most of them did not respond to training.}, }
@article {pmid35001263, year = {2022}, author = {Zhang, X and Linghu, S and Chen, Z and Gu, H and Chen, X and Wei, X and Hu, X and Yang, Y and Gao, Y}, title = {Bacterial diversity evolution process based on physicochemical characteristics of sludge treating hydroquinone during acclimation.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {35001263}, issn = {1614-7499}, abstract = {Hydroquinone is one of the main pollutants in coal-gasification wastewater, which is biologically toxic and difficult to remove. The aerobic biodegradation rate, organic toxicity, and microbial community structure at different acclimation stages of degradation of hydroquinone by activated sludge were investigated. In each acclimation cycle, the removal of hydroquinone reached 100% after 5 days, indicating that high-concentration hydroquinone in the activated sludge could be completely biodegraded. When the microbial flora was inhibited by the influent hydroquinone, the enzyme system experienced stress conditions and led to the secretion of secondary metabolites, extracellular protein of 5-10 kDa mainly contributing to the sludge organic toxicity. Microbial diversity analysis showed that with the increase of the concentration of hydroquinone, β-Proteus bacteria such as Azoarcus and Dechloromonas gradually accumulated, which improved the removal of hydroquinone with aerobic activated sludge in the sequencing batch reactor (SBR) system. As the inhibition degree exceeded the appropriate tolerance range of microorganisms, bacteria would secrete much more secondary metabolites, and the organic toxicity of sludge would reach a relatively high level.}, }
@article {pmid35000310, year = {2022}, author = {Zou, XH and Cao, B}, title = {[Advances in pathogen diagnosis of respiratory infection diseases in 2021].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {45}, number = {1}, pages = {78-82}, doi = {10.3760/cma.j.cn112147-20211116-00809}, pmid = {35000310}, issn = {1001-0939}, support = {81900009, 82041011, 82030002//National Natural Science Foundation of China/ ; Z191100006619101//Beijing Municipal Science &amp; Technology Commission/ ; 2020-I2M-CoV19-005//Chinese Acadamy of Medical Sciences Innovation Fund for Medical Sciences/ ; }, abstract = {Respiratory tract infections (RTI) are a common and highly prevalent disease in the population, which can develop into acute respiratory distress syndrome (ARDS) in severe cases.A large variety of microorganisms can cause RTI, including bacteria, respiratory viruses, and fungi. The timely and accurate detection of these pathogens is the prerequisites of effective treatment of RTI. However, more than 50% of RTI patients failed to diagnosis of causative agents due to unavailability of qualified samples, antimicrobial treatment prior to sample collection, high variety of respiratory pathogens, and influence of the normal flora in respiratory tract. In recent years, progress on molecular diagnosis, especially the novel approaches such as clinical metagenomics and CRSIPR (Clustered regularly interspaced short palindromic repeats), has not only improved our capacity for RTI pathogen detection but also brought new challenges. In this review, we summed up the advances in RTI pathogen diagnosis in 2021 and discussed the clinical benefits and challenges from novel approaches, which provided a clinical perspective on the development and application of these diagnostic tools in the real world.}, }
@article {pmid34999397, year = {2021}, author = {Chang, HM and Chen, SS and Hsiao, SS and Chang, WS and Chien, IC and Duong, CC and Nguyen, TXQ}, title = {Water reclamation and microbial community investigation: Treatment of tetramethylammonium hydroxide wastewater through an anaerobic osmotic membrane bioreactor hybrid system.}, journal = {Journal of hazardous materials}, volume = {427}, number = {}, pages = {128200}, doi = {10.1016/j.jhazmat.2021.128200}, pmid = {34999397}, issn = {1873-3336}, abstract = {Tetramethylammonium hydroxide (TMAH) is a toxic photoresist developer used in the photolithography process in thin-film transistor liquid crystal display (TFT-LCD) production, and it can be removed through anaerobic treatment. TMAH cannot be released into the environment because of its higher toxicity. A tight membrane, such as a forward osmosis (FO) membrane, together with an anaerobic biological process can ensure that no TMAH is released into the environment. Thus, for the first time, an anaerobic osmotic membrane bioreactor (AnOMBR) hybrid system was developed in this study to treat a low-strength TMAH wastewater and to simultaneously investigate its microbial community. Microfiltration extraction was used to mitigate the salinity accumulation, and a periodically physical water cleaning was utilized to mitigate the FO membrane fouling. The diluted draw solute (MgSO4) was reconcentrated and reused by a membrane distillation (MD) process in the AnOMBR to achieve 99.99% TMAH removal in this AnOMBR-MD hybrid system, thereby ensuring that no TMAH is released into the natural environment. Moreover, the membrane fouling in the feed and draw sides were analyzed through the fluorescence excitation-emission matrix (FEEM) spectrophotometry to confirm that the humic acid-like materials were the primary membrane fouling components in this AnOMBR. Additionally, 16S rRNA metagenomics analysis indicated that Methanosaeta was the predominant contributor to methanogenesis and proliferated during the long-term operation. The methane yield was increased from 0.2 to 0.26 L CH4/g COD when the methanogen species acclimatized to the saline system.}, }
@article {pmid34998910, year = {2022}, author = {Liew, WP and Sabran, MR and Than, LT and Abd-Ghani, F}, title = {Metagenomic and proteomic approaches in elucidating aflatoxin B1 detoxification mechanisms of probiotic Lactobacillus casei Shirota towards intestine.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {}, number = {}, pages = {112808}, doi = {10.1016/j.fct.2022.112808}, pmid = {34998910}, issn = {1873-6351}, abstract = {The modulation of gut microbiota and proteome due to aflatoxin B1 (AFB1) by probiotics remains unclear. This study investigated the alterations of gut microbiota and proteome in AFB1-exposed rats treated with probiotic Lactobacillus casei Shirota (Lcs). Forty male Sprague Dawley rats were randomly divided into five groups (n = 8) comprised control, AFB1, AFB1+activated charcoal, AFB1+Lcs, and Lcs groups. The rats were subjected to different treatments via oral gavage for four weeks. Urine and serum were collected for the measurement of AFB1 biomarkers and organs were harvested for histological analysis. Metagenomic sequencing was performed on fecal samples to profile gut microbiota. Besides, AFB1 most affected organ i.e. jejunum was subjected to proteomic analysis. The results indicated that Lcs intervention significantly reduced AFB1 biomarkers. H&amp;E-stained intestine showed Lcs alleviated AFB1-induced inflammation and abnormal cell growth, particularly at the jejunum. Although AFB1 increased potentially pathogenic bacteria and reduced beneficial bacteria abundance in feces, the microbiota composition was normalized with Lcs treatment. The gut proteome analysis of the jejunum sample showed several pathways of AFB1 toxicity, wherein Lcs treatment demonstrated its protective effect. It is concluded that metagenomic and proteomic approaches are useful tools to understand AFB1-Lcs interaction and detoxification mechanism in the gut.}, }
@article {pmid34998802, year = {2022}, author = {Pratt, M and Forbes, JD and Knox, NC and Van Domselaar, G and Bernstein, CN}, title = {Colorectal cancer screening in IBD - can characterization of GI microbiome signatures enhance neoplasia detection?.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2021.12.287}, pmid = {34998802}, issn = {1528-0012}, abstract = {Current non-invasive CRC screening methods are not optimized for persons with IBD, requiring patients to undergo frequent interval screening via colonoscopy. Although colonoscopy-based screening reduces CRC incidence in IBD patients, rates of interval CRC remain relatively high, highlighting the need for more targeted approaches. In recent years, the discovery of disease-specific microbiome signatures for both IBD and CRC has begun to emerge, suggesting that stool-based biomarker detection using metagenomics and other culture-independent technologies may be useful for personalized, early, non-invasive CRC screening in IBD patients. Here we discuss the utility of the stool microbiome as a non-invasive CRC screening tool. Comparing the performance of multiple microbiome-based CRC classifiers, including several multi-cohort meta-analyses, we find that non-invasive detection of colorectal adenomas and carcinomas from microbial biomarkers is an active area of study with promising early results.}, }
@article {pmid34998377, year = {2022}, author = {Zhang, Y and Zhang, H and Deng, B and Lin, K and Jin, L and Liu, X and Zhang, Y and Chen, X and Zhang, Y and Lu, S and Huang, H and Wang, Q and Feng, T and Zhao, W and Xue, Q and Chen, R and Zhang, J and Qian, X and Chen, L and Ai, J and Chen, X and Zhang, W}, title = {Optimal encephalitis/meningitis roadmap via precise diagnosis and treatment (IMPROVE): a study protocol for a randomized controlled trial.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {40}, pmid = {34998377}, issn = {1471-2334}, support = {82002141//Young Scientists Fund/ ; 20dz2260100//Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response/ ; GWV-10.1-XK01//Key Discipline Construction Plan from Shanghai Municipal Health Commission/ ; }, abstract = {BACKGROUND: Encephalitis/meningitis brings a heavy disease burden, and the origin of disease remains unknown in 30-40% of patients. It is greatly significant that combinations of nucleic acid amplification and autoimmune antibody testing improves the diagnosis and treatment of encephalitis/meningitis. Moreover, though several diagnostic methods are in clinical use, a recognized and unified diagnosis and treatment process for encephalitis management remains unclear.<br><br>METHODS: IMPROVE is a multicenter, open label, randomized controlled clinical trial that aims to evaluate the diagnostic performance, applications, and impact on patient outcomes of a new diagnostic algorithm that combines metagenomic next-generation sequencing (mNGS), multiplex polymerase chain reaction (PCR) and autoimmune antibody testing. The enrolled patients will be grouped into two parallel groups, multiplex PCR test plus autoimmune antibody group (Group I) or the mNGS plus autoimmune antibody group (Group II) with a patient ratio of 1:1. Both groups will be followed up for 12 months. The primary outcomes include the initial time of targeted treatment and the modified Rankin scale score on the 30th day of the trial. The secondary outcomes are the cerebrospinal fluid index remission rate on the 14th day, mortality rate on the 30th day, and an evaluation of diagnostic efficacy. The two groups are predicted to comprise of 484 people in total.<br><br>DISCUSSION: To optimize the roadmap of encephalitis/meningitis, precise diagnosis, and treatment are of great significance. The effect of rapid diagnosis undoubtedly depends on the progression of new diagnostic tests, such as the new multiplex PCR, mNGS, and examination of broad-spectrum autoimmune encephalitis antibodies. This randomized-controlled study could allow us to obtain an accurate atlas of the precise diagnostic ability of these tests and their effect on the treatment and prognosis of patients. Trial registration ClinicalTrial.gov, NCT04946682. Registered 29 June 2021, 'Retrospectively registered', https://clinicaltrials.gov/ct2/show/NCT04946682?term=NCT04946682&amp;draw=2&amp;rank=1.}, }
@article {pmid34880234, year = {2021}, author = {Murchie, TJ and Monteath, AJ and Mahony, ME and Long, GS and Cocker, S and Sadoway, T and Karpinski, E and Zazula, G and MacPhee, RDE and Froese, D and Poinar, HN}, title = {Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {7120}, pmid = {34880234}, issn = {2041-1723}, mesh = {Animals ; Canada ; Climate Change ; *DNA, Ancient ; *DNA, Environmental ; Ecosystem ; Equidae/genetics ; Fossils ; Horses/genetics ; Human Activities ; Mammoths/*genetics ; Metagenome ; Plants/genetics ; Yukon Territory ; }, abstract = {The temporal and spatial coarseness of megafaunal fossil records complicates attempts to to disentangle the relative impacts of climate change, ecosystem restructuring, and human activities associated with the Late Quaternary extinctions. Advances in the extraction and identification of ancient DNA that was shed into the environment and preserved for millennia in sediment now provides a way to augment discontinuous palaeontological assemblages. Here, we present a 30,000-year sedimentary ancient DNA (sedaDNA) record derived from loessal permafrost silts in the Klondike region of Yukon, Canada. We observe a substantial turnover in ecosystem composition between 13,500 and 10,000 calendar years ago with the rise of woody shrubs and the disappearance of the mammoth-steppe (steppe-tundra) ecosystem. We also identify a lingering signal of Equus sp. (North American horse) and Mammuthus primigenius (woolly mammoth) at multiple sites persisting thousands of years after their supposed extinction from the fossil record.}, }
@article {pmid34864063, year = {2022}, author = {Pradhan, S and Ray, P and Aich, P}, title = {Microbiota transplantation from younger to older mice could restore lost immunity to effectively clear salmonella infection in Th2-biased BALB/c mice.}, journal = {Life sciences}, volume = {288}, number = {}, pages = {120201}, doi = {10.1016/j.lfs.2021.120201}, pmid = {34864063}, issn = {1879-0631}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*growth &amp; development ; Cecum/*transplantation ; Fecal Microbiota Transplantation/*methods ; Gastrointestinal Microbiome ; Homeostasis ; Immunity, Innate ; Male ; Metabolome ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Salmonella/drug effects/genetics/*immunology/metabolism ; Salmonella Infections/immunology/metabolism/microbiology/*therapy ; Th2 Cells/*immunology ; }, abstract = {AIMS: The composition, overtly abundance, and diversity of gut microbiota, play a significant role in maintaining physiological homeostasis with age. Reports revealed that the gut microbial profile might be correlated with immunity and metabolism. It is, therefore, tantamount to know if an older individual can achieve the immunity and metabolic profile of a younger individual by receiving the gut microbiome of a younger individual. In the current report, we have studied the effects of cecal microbiota transplantation (CMT) from younger to older mice.<br><br>MATERIALS AND METHODS: In this study, older BALB/c mice (23 weeks) received CMT from younger BALB/c mice (3 weeks).<br><br>KEY FINDINGS: CMT recipient mice showed altered expressions of immune and tight junction protein genes in the colon of mice, while the non-CMT recipient mice did not. Older mice were treated with AVNM to make them compatible with CMT. Further data from metabolite studies revealed that AVNM treatment mainly affected the aromatic amino acid biosynthesis pathway while CMT mostly affected the metabolism of different carbohydrates. We repeated the analysis in C57BL/6 mice without any significant effects of CMT.<br><br>SIGNIFICANCE: Results revealed that mice who received CMT showed more efficient restoration of gut microbiota than non-CMT recipient mice. CMT caused the alleviation of Salmonella infection and efficient recovery of the cecal index in the mice following antibiotics treatment.}, }
@article {pmid34341764, year = {2021}, author = {Wen, M and Liu, T and Zhao, M and Dang, X and Feng, S and Ding, X and Xu, Z and Huang, X and Lin, Q and Xiang, W and Li, X and He, X and He, Q}, title = {Correlation Analysis between Gut Microbiota and Metabolites in Children with Systemic Lupus Erythematosus.}, journal = {Journal of immunology research}, volume = {2021}, number = {}, pages = {5579608}, pmid = {34341764}, issn = {2314-7156}, mesh = {Age Factors ; Biomarkers ; Case-Control Studies ; Child ; *Disease Susceptibility ; Dysbiosis ; Feces/microbiology ; Female ; Gas Chromatography-Mass Spectrometry/methods ; *Gastrointestinal Microbiome ; Humans ; Immunosuppressive Agents/therapeutic use ; Lupus Erythematosus, Systemic/drug therapy/*etiology/*metabolism/pathology ; Male ; *Metabolome ; Metabolomics/methods ; Metagenomics/methods ; }, abstract = {Systemic lupus erythematosus (SLE) is an autoimmune-mediated diffuse connective tissue disease characterized by immune inflammation with an unclear aetiology and pathogenesis. This work profiled the intestinal flora and faecal metabolome of patients with SLE using 16S RNA sequencing and gas chromatography-mass spectrometry (GC-MS). We identified unchanged alpha diversity and partially altered beta diversity of the intestinal flora. Another important finding was the increase in Proteobacteria and Enterobacteriales and the decrease in Ruminococcaceae among SLE patients. For metabolites, amino acids and short-chain fatty acids were enriched when long-chain fatty acids were downregulated in SLE faecal samples. KEGG analysis showed the significance of the protein digestion and absorption pathway, and association analysis revealed the key role of 3-phenylpropanoic acid and Sphingomonas. Sphingomonas were reported to be less abundant in healthy periodontal sites of SLE patients than in those of HCs, indicating transmission of oral species to the gut. This study contributes to the understanding of the pathogenesis of SLE disease from the perspective of intestinal microorganisms, explains the pathogenesis of SLE, and serves as a basis for exploring potential treatments for the disease.}, }
@article {pmid33779498, year = {2021}, author = {Kang, K and Imamovic, L and Misiakou, MA and Bornakke Sørensen, M and Heshiki, Y and Ni, Y and Zheng, T and Li, J and Ellabaan, MMH and Colomer-Lluch, M and Rode, AA and Bytzer, P and Panagiotou, G and Sommer, MOA}, title = {Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment.}, journal = {Gut microbes}, volume = {13}, number = {1}, pages = {1-19}, pmid = {33779498}, issn = {1949-0984}, mesh = {Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/*therapeutic use ; Bacteria/virology ; Bacteriophages/drug effects ; Biological Warfare ; Cohort Studies ; *Drug Resistance, Microbial ; Feces/*microbiology/*virology ; Gastrointestinal Microbiome/*drug effects ; Gene Transfer, Horizontal/drug effects ; Humans ; Metagenome/drug effects ; Microbiota/*drug effects ; Middle Aged ; Plasmids/drug effects ; Transcriptome/drug effects ; Virome/drug effects ; Young Adult ; }, abstract = {Oral antibiotics are commonly prescribed to non-hospitalized adults. However, antibiotic-induced changes in the human gut microbiome are often investigated in cohorts with preexisting health conditions and/or concomitant medication, leaving the effects of antibiotics not completely understood. We used a combination of omic approaches to comprehensively assess the effects of antibiotics on the gut microbiota and particularly the gut resistome of a small cohort of healthy adults. We observed that 3 to 19 species per individual proliferated during antibiotic treatment and Gram-negative species expanded significantly in relative abundance. While the overall relative abundance of antibiotic resistance gene homologs did not significantly change, antibiotic-specific gene homologs with presumed resistance toward the administered antibiotics were common in proliferating species and significantly increased in relative abundance. Virome sequencing and plasmid analysis showed an expansion of antibiotic-specific resistance gene homologs even 3 months after antibiotic administration, while paired-end read analysis suggested their dissemination among different species. These results suggest that antibiotic treatment can lead to a persistent expansion of antibiotic resistance genes in the human gut microbiota and provide further data in support of good antibiotic stewardship.Abbreviation: ARG - Antibiotic resistance gene homolog; AsRG - Antibiotic-specific resistance gene homolog; AZY - Azithromycin; CFX - Cefuroxime; CIP - Ciprofloxacin; DOX - Doxycycline; FDR - False discovery rate; GRiD - Growth rate index value; HGT - Horizontal gene transfer; NMDS - Non-metric multidimensional scaling; qPCR - Quantitative polymerase chain reaction; RPM - Reads per million mapped reads; TA - Transcriptional activity; TE - Transposable element; TPM - Transcripts per million mapped reads.}, }
@article {pmid34997305, year = {2022}, author = {Ragot, R and Villemur, R}, title = {eDNA profiling of mammals, birds, and fish of surface waters by mitochondrial metagenomics: application for source tracking of fecal contamination in surface waters.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {2}, pages = {72}, pmid = {34997305}, issn = {1573-2959}, support = {RGPIN-2016-06061//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Knowing the composition of animals present in aquatic ecosystems can tell us about the anthropic pressures on these environments. One of these pressures is the occurrence of fecal contamination. However, this contamination can originate from more than one animal species in areas where urban and agricultural activities overlap. Mitochondrial DNA (mtDNA) has become the standard barcoding tool to identify the presence of animal species in environment. Amplicon-sequencing metagenomics is a powerful approach to derive the animal profile in an environment. However, PCR primers targeting mtDNA of a broad range of animals are highly degenerate or generate short DNA fragments that could cause ambiguous affiliation. Here we report the development of a new set of primers targeting the mitochondrial 16S ribosomal RNA genes of a broad range of terrestrial and aquatic animals, which include mammals, birds, and fishes. These primers successfully amplified mtDNA from environmental DNA (eDNA) extracted from surface waters. Sequencing the resulting amplicons revealed the presence of mammals and birds that may contribute in fecal contamination of surface water. In one of the river samples high in fecal indicator bacteria, human and bovine mtDNA accounted for 40.5% and 4.1% of the sequences, respectively, suggesting fecal contamination by these two animals. These findings indicate that our PCR primers coupled with amplicon-sequencing metagenomics contribute in profiling the animal diversity in the surface waters and its surrounding. This approach could be a valuable tool to identify simultaneously the potential contribution of various animals as sources of fecal contamination in surface waters.}, }
@article {pmid34997042, year = {2022}, author = {Phan, MVT and Agoti, CN and Munywoki, PK and Otieno, GP and Ngama, M and Kellam, P and Cotten, M and Nokes, DJ}, title = {Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {202}, pmid = {34997042}, issn = {2045-2322}, support = {102975/WT_/Wellcome Trust/United Kingdom ; 090853/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Pneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus diagnostics in Kilifi, Kenya, using random-primed viral next generation sequencing (viral NGS) on respiratory samples which tested negative for the common viral respiratory pathogens by a local standard diagnostic panel. Among 95 hospitalised pneumonia patients and 95 household-cohort individuals, analysis of viral NGS identified at least one respiratory-associated virus in 35 (37%) and 23 (24%) samples, respectively. The majority (66%; 42/64) belonged to the Picornaviridae family. The NGS data analysis identified a number of viruses that were missed by the diagnostic panel (rhinovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus), and these failures could be attributed to PCR primer/probe binding site mismatches. Unexpected viruses identified included parvovirus B19, enterovirus D68, coxsackievirus A16 and A24 and rubella virus. The regular application of such viral NGS could help evaluate assay performance, identify molecular causes of missed diagnoses and reveal gaps in the respiratory virus set used for local screening assays. The results can provide actionable information to improve the local pneumonia diagnostics and reveal locally important viral pathogens.}, }
@article {pmid34996879, year = {2022}, author = {Chen, SJ and Chen, CC and Liao, HY and Lin, YT and Wu, YW and Liou, JM and Wu, MS and Kuo, CH and Lin, CH}, title = {Association of Fecal and Plasma Levels of Short-Chain Fatty Acids With Gut Microbiota and Clinical Severity in Parkinson Disease Patients.}, journal = {Neurology}, volume = {}, number = {}, pages = {}, doi = {10.1212/WNL.0000000000013225}, pmid = {34996879}, issn = {1526-632X}, abstract = {BACKGROUND AND OBJECTIVES: Short-chain fatty acids (SCFAs) are gut microbial metabolites that promote the disease process in a rodent model of Parkinson's disease (PD), but fecal levels of SCFAs in PD patients are reduced. Simultaneous assessments of fecal and plasma SCFA levels, and their inter-relationships with the PD disease process are scarce. We aimed to compare fecal and plasma levels of different SCFAs subtypes in PD patients and healthy controls to delineate their interrelations and link to gut microbiota changes and clinical severity of PD.<br><br>METHODS: A cohort of 96 PD patients and 85 controls were recruited from National Taiwan University Hospital. Fecal and plasma concentrations of SCFAs were measured using chromatography and mass spectrometry. Gut microbiota was analyzed using metagenomic shotgun sequencing. Body mass index and medical co-morbidities were evaluated, and dietary information was obtained using a food frequency questionnaire. To assess motor and cognitive impairment, we used the Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and the Mini-Mental Status Examination (MMSE).<br><br>RESULTS: Compared with controls, PD patients had lower fecal but higher plasma concentrations of acetate, propionate, and butyrate. After adjustment for age, sex, disease duration, and anti-PD medication dosage, MDS-UPDRS part III motor scores correlated with reduced fecal levels of acetate (ρ = -0.37, p = 0.012), propionate (ρ = -0.32, p = 0.036), and butyrate (ρ = -0.40, p = 0.004) and with increased plasma propionate concentrations (ρ = 0.26, p = 0.042) in PD patients. MMSE scores negatively correlated with plasma levels of butyrate (ρ = -0.09, p = 0.027) and valerate (ρ = -0.032, p = 0.033) after adjustment for confounders. SCFAs-producing gut bacteria correlated positively with fecal levels of SCFAs in healthy controls but revealed no association in patients with PD. In the PD patient group, the abundance of pro-inflammatory microbes, such as Clostridiales bacterium NK3B98 and Ruminococcus sp. AM07-15, significantly correlated with decreased fecal levels and increased plasma levels of SCFAs, especially propionic acid.<br><br>DISCUSSION: Reductions in fecal SCFAs but increased plasma SCFAs were observed in PD patients and corelated to specific gut microbiota changes and the clinical severity of PD.<br><br>CLASSIFICATION OF EVIDENCE: This study provides Class III evidence that gut metabolite SCFAs distinguish between PD patients and controls, and are associated with disease severity in patients with PD.}, }
@article {pmid34996709, year = {2021}, author = {Zhan, Z and Li, CF and Liu, J and Cao, CS and Huang, L}, title = {Metagenomic next-generation sequencing to diagnose atypical severe scrub typhus.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2021.12.002}, pmid = {34996709}, issn = {1995-9133}, }
@article {pmid34996363, year = {2022}, author = {Jia, B and Chang, X and Fu, Y and Heng, W and Ye, Z and Liu, P and Liu, L and Al Shoffe, Y and Watkins, CB and Zhu, L}, title = {Metagenomic analysis of rhizosphere microbiome provides insights into occurrence of iron deficiency chlorosis in field of Asian pears.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {18}, pmid = {34996363}, issn = {1471-2180}, abstract = {BACKGROUND: Fe-deficiency chlorosis (FDC) of Asian pear plants is widespread, but little is known about the association between the microbial communities in the rhizosphere soil and leaf chlorosis. The leaf mineral concentration, leaf subcellular structure, soil physiochemical properties, and bacterial species community and distribution had been analysed to gain insights into the FDC in Asian pear plant.<br><br>RESULTS: The total Fe in leaves with Fe-deficiency was positively correlated with total K, Mg, S, Cu, Zn, Mo and Cl contents, but no differences of available Fe (AFe) were detected between the rhizosphere soil of chlorotic and normal plants. Degraded ribosomes and degraded thylakloid stacks in chloroplast were observed in chlorotic leaves. The annotated microbiome indicated that there were 5 kingdoms, 52 phyla, 94 classes, 206 orders, 404 families, 1,161 genera, and 3,043 species in the rhizosphere soil of chlorotic plants; it was one phylum less and one order, 11 families, 59 genera, and 313 species more than in that of normal plant. Bacterial community and distribution patterns in the rhizosphere soil of chlorotic plants were distinct from those of normal plants and the relative abundance and microbiome diversity were more stable in the rhizosphere soils of normal than in chlorotic plants. Three (Nitrospira defluvii, Gemmatirosa kalamazoonesis, and Sulfuricella denitrificans) of the top five species (N. defluvii, G. kalamazoonesis, S. denitrificans, Candidatus Nitrosoarchaeum koreensis, and Candidatus Koribacter versatilis). were the identical and aerobic in both rhizosphere soils, but their relative abundance decreased by 48, 37, and 22%, respectively, and two of them (G. aurantiaca and Ca. S. usitatus) were substituted by an ammonia-oxidizing soil archaeon, Ca. N. koreensis and a nitrite and nitrate reduction related species, Ca. K. versatilis in that of chlorotic plants, which indicated the adverse soil aeration in the rhizosphere soil of chlorotic plants. A water-impermeable tables was found to reduce the soil aeration, inhibit root growth, and cause some absorption root death from infection by Fusarium solani.<br><br>CONCLUSIONS: It was waterlogging or/and poor drainage of the soil may inhibit Fe uptake not the amounts of AFe in the rhizosphere soil of chlorotic plants that caused FDC in this study.}, }
@article {pmid34996356, year = {2022}, author = {Xu, G and Zhang, L and Liu, X and Guan, F and Xu, Y and Yue, H and Huang, JQ and Chen, J and Wu, N and Tian, J}, title = {Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {37}, pmid = {34996356}, issn = {1471-2164}, abstract = {BACKGROUND: Advances in DNA sequencing technologies have transformed our capacity to perform life science research, decipher the dynamics of complex soil microbial communities and exploit them for plant disease management. However, soil is a complex conglomerate, which makes functional metagenomics studies very challenging.<br><br>RESULTS: Metagenomes were assembled by long-read (PacBio, PB), short-read (Illumina, IL), and mixture of PB and IL (PI) sequencing of soil DNA samples were compared. Ortholog analyses and functional annotation revealed that the PI approach significantly increased the contig length of the metagenomic sequences compared to IL and enlarged the gene pool compared to PB. The PI approach also offered comparable or higher species abundance than either PB or IL alone, and showed significant advantages for studying natural product biosynthetic genes in the soil microbiomes.<br><br>CONCLUSION: Our results provide an effective strategy for combining long and short-read DNA sequencing data to explore and distill the maximum information out of soil metagenomics.}, }
@article {pmid34996352, year = {2022}, author = {Jiang, M and Xu, SF and Tang, TS and Miao, L and Luo, BZ and Ni, Y and Kong, FD and Liu, C}, title = {Development and evaluation of a meat mitochondrial metagenomic (3MG) method for composition determination of meat from fifteen mammalian and avian species.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {36}, pmid = {34996352}, issn = {1471-2164}, abstract = {BACKGROUND: Bioassessment and biomonitoring of meat products are aimed at identifying and quantifying adulterants and contaminants, such as meat from unexpected sources and microbes. Several methods for determining the biological composition of mixed samples have been used, including metabarcoding, metagenomics and mitochondrial metagenomics. In this study, we aimed to develop a method based on next-generation DNA sequencing to estimate samples that might contain meat from 15 mammalian and avian species that are commonly related to meat bioassessment and biomonitoring.<br><br>RESULTS: In this project, we found the meat composition from 15 species could not be identified with the metabarcoding approach because of the lack of universal primers or insufficient discrimination power. Consequently, we developed and evaluated a meat mitochondrial metagenomics (3MG) method. The 3MG method has four steps: (1) extraction of sequencing reads from mitochondrial genomes (mitogenomes); (2) assembly of mitogenomes; (3) mapping of mitochondrial reads to the assembled mitogenomes; and (4) biomass estimation based on the number of uniquely mapped reads. The method was implemented in a python script called 3MG. The analysis of simulated datasets showed that the method can determine contaminant composition at a proportion of 2% and the relative error was < 5%. To evaluate the performance of 3MG, we constructed and analysed mixed samples derived from 15 animal species in equal mass. Then, we constructed and analysed mixed samples derived from two animal species (pork and chicken) in different ratios. DNAs were extracted and used in constructing 21 libraries for next-generation sequencing. The analysis of the 15 species mix with the method showed the successful identification of 12 of the 15 (80%) animal species tested. The analysis of the mixed samples of the two species revealed correlation coefficients of 0.98 for pork and 0.98 for chicken between the number of uniquely mapped reads and the mass proportion.<br><br>CONCLUSION: To the best of our knowledge, this study is the first to demonstrate the potential of the non-targeted 3MG method as a tool for accurately estimating biomass in meat mix samples. The method has potential broad applications in meat product safety.}, }
@article {pmid34995880, year = {2022}, author = {Fernandez-Cassi, X and Timoneda, N and Martínez-Puchol, S and Rusiñol, M and Rodriguez-Manzano, J and Figuerola, N and Bofill-Mas, S and Abril, JF and Girones, R}, title = {Corrigendum to "Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance" [Sci. Total Environ. 618 (2016) 870-880 10.1016/j.scitotenv.2017.08.249].}, journal = {The Science of the total environment}, volume = {814}, number = {}, pages = {152530}, doi = {10.1016/j.scitotenv.2021.152530}, pmid = {34995880}, issn = {1879-1026}, }
@article {pmid34995620, year = {2022}, author = {Liu, J and Liu, Y and Dong, W and Li, J and Yu, S and Wang, J and Zuo, R}, title = {Shifts in microbial community structure and function in polycyclic aromatic hydrocarbon contaminated soils at petrochemical landfill sites revealed by metagenomics.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {133509}, doi = {10.1016/j.chemosphere.2021.133509}, pmid = {34995620}, issn = {1879-1298}, abstract = {Investigations of the microbial community structures, potential functions and polycyclic aromatic hydrocarbon (PAH) degradation-related genes in PAH-polluted soils are useful for risk assessments, microbial monitoring, and the potential bioremediation of soils polluted by PAHs. In this study, five soil sampling sites were selected at a petrochemical landfill in Beijing, China, to analyze the contamination characteristics of PAHs and their impact on microorganisms. The concentrations of 16 PAHs were detected by gas chromatography-mass spectrometry. The total concentrations of the PAHs ranged from ND to 3166.52 μg/kg, while phenanthrene, pyrene, fluoranthene and benzo[ghi]perylene were the main components in the soil samples. According to the specific PAH ratios, the PAHs mostly originated from petroleum wastes in the landfill. The levels of the total toxic benzo[a]pyrene equivalent (1.63-107.73 μg/kg) suggested that PAHs might result in adverse effects on soil ecosystems. The metagenomic analysis showed that the most abundant phyla in the soils were Proteobacteria and Actinobacteria, and Solirubrobacter was the most important genus. At the genus level, Bradyrhizobium, Mycobacterium and Anaeromyxobacter significantly increased under PAH stress. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, the most abundant category of functions that are involved in adapting to contaminant pressures was identified. Ten PAH degradation-related genes were significantly influenced by PAH pressure and showed correlations with PAH concentrations. All of the results suggested that the PAHs from the petrochemical landfill could be harmful to soil environments and impact the soil microbial community structures, while microorganisms would change their physiological functions to resist pollutant stress.}, }
@article {pmid34995411, year = {2022}, author = {Fuchsman, CA and Cherubini, L and Hays, MD}, title = {An Analysis of Protists in Pacific Oxygen Deficient Zones: Implications for Prochlorococcus and N2 producing bacteria.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15893}, pmid = {34995411}, issn = {1462-2920}, abstract = {Ocean oxygen deficient zones (ODZs) host 30-50% of marine N2 production. Cyanobacteria photosynthesizing in the ODZ create a secondary chlorophyll maximum and provide organic matter to N2 producing bacteria. This chlorophyll maximum is thought to occur due to reduced grazing in anoxic waters. We first examine ODZ protists with long amplicon reads. We then use non-primer-based methods to examine the composition and relative abundance of protists in metagenomes from the Eastern Tropical North and South Pacific ODZs and compare these data to the oxic Hawaii Ocean Time-series in the North Pacific. We identify and quantify protists in proportion to the total microbial community. From metagenomic data, we see a large drop in abundance of fungi and protists such as choanoflagellates, radiolarians, cercozoa and ciliates in the ODZs but not in the oxic mesopelagic at HOT. Diplonemid euglenozoa were the only protists that increased in the ODZ. Dinoflagellates and foraminifera reads were also present in the ODZ though less abundant compared to oxic waters. Denitrification has been found in foraminifera but not yet in dinoflagellates. DNA techniques cannot separate dinoflagellate cells and cysts. Metagenomic analysis found taxonomic groups missed by amplicon sequencing and identified trends in abundance. This article is protected by copyright. All rights reserved.}, }
@article {pmid34995388, year = {2022}, author = {Nappi, J and Goncalves, P and Khan, T and Majzoub, ME and Grobler, AS and Marzinelli, EM and Thomas, T and Egan, S}, title = {Differential priority effects impact taxonomy and functionality of host-associated microbiomes.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16336}, pmid = {34995388}, issn = {1365-294X}, abstract = {Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g. depletion of Type III Secretion System genes) and unique (e.g. enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.}, }
@article {pmid34993013, year = {2021}, author = {Torres-Beltrán, M and Vargas-Gastélum, L and Magdaleno-Moncayo, D and Riquelme, M and Herguera-García, JC and Prieto-Davó, A and Lago-Lestón, A}, title = {The metabolic core of the prokaryotic community from deep-sea sediments of the southern Gulf of Mexico shows different functional signatures between the continental slope and abyssal plain.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12474}, doi = {10.7717/peerj.12474}, pmid = {34993013}, issn = {2167-8359}, abstract = {Marine sediments harbor an outstanding level of microbial diversity supporting diverse metabolic activities. Sediments in the Gulf of Mexico (GoM) are subjected to anthropic stressors including oil pollution with potential effects on microbial community structure and function that impact biogeochemical cycling. We used metagenomic analyses to provide significant insight into the potential metabolic capacity of the microbial community in Southern GoM deep sediments. We identified genes for hydrocarbon, nitrogen and sulfur metabolism mostly affiliated with Alpha and Betaproteobacteria, Acidobacteria, Chloroflexi and Firmicutes, in relation to the use of alternative carbon and energy sources to thrive under limiting growth conditions, and metabolic strategies to cope with environmental stressors. In addition, results show amino acids metabolism could be associated with sulfur metabolism carried out by Acidobacteria, Chloroflexi and Firmicutes, and may play a crucial role as a central carbon source to favor bacterial growth. We identified the tricarboxylic acid cycle (TCA) and aspartate, glutamate, glyoxylate and leucine degradation pathways, as part of the core carbon metabolism across samples. Further, microbial communities from the continental slope and abyssal plain show differential metabolic capacities to cope with environmental stressors such as oxidative stress and carbon limiting growth conditions, respectively. This research combined taxonomic and functional information of the microbial community from Southern GoM sediments to provide fundamental knowledge that links the prokaryotic structure to its potential function and which can be used as a baseline for future studies to model microbial community responses to environmental perturbations, as well as to develop more accurate mitigation and conservation strategies.}, }
@article {pmid34991704, year = {2022}, author = {Pickering, H and Hart, JD and Burr, S and Stabler, R and Maleta, K and Kalua, K and Bailey, RL and Holland, MJ}, title = {Impact of azithromycin mass drug administration on the antibiotic-resistant gut microbiome in children: a randomized, controlled trial.}, journal = {Gut pathogens}, volume = {14}, number = {1}, pages = {5}, pmid = {34991704}, issn = {1757-4749}, support = {OPP1066930//Bill and Melinda Gates Foundation/ ; OP1032340//Bill and Melinda Gates Foundation/ ; }, abstract = {BACKGROUND: Mass drug administration (MDA) with azithromycin is the primary strategy for global trachoma control efforts. Numerous studies have reported secondary effects of MDA with azithromycin, including reductions in childhood mortality, diarrhoeal disease and malaria. Most recently, the MORDOR clinical trial demonstrated that MDA led to an overall reduction in all-cause childhood mortality in targeted communities. There is however concern about the potential of increased antimicrobial resistance in treated communities. This study evaluated the impact of azithromycin MDA on the prevalence of gastrointestinal carriage of macrolide-resistant bacteria in communities within the MORDOR Malawi study, additionally profiling changes in the gut microbiome after treatment. For faecal metagenomics, 60 children were sampled prior to treatment and 122 children after four rounds of MDA, half receiving azithromycin and half placebo.<br><br>RESULTS: The proportion of bacteria carrying macrolide resistance increased after azithromycin treatment. Diversity and global community structure of the gut was minimally impacted by treatment, however abundance of several species was altered by treatment. Notably, the putative human enteropathogen Escherichia albertii was more abundant after treatment.<br><br>CONCLUSIONS: MDA with azithromycin increased carriage of macrolide-resistant bacteria, but had limited impact on clinically relevant bacteria. However, increased abundance of enteropathogenic Escherichia species after treatment requires further, higher resolution investigation. Future studies should focus on the number of treatments and administration schedule to ensure clinical benefits continue to outweigh costs in antimicrobial resistance carriage. Trial registration ClinicalTrial.gov, NCT02047981. Registered January 29th 2014, https://clinicaltrials.gov/ct2/show/NCT02047981.}, }
@article {pmid34991519, year = {2022}, author = {Zhou, Y and Liu, Y and Wen, Y}, title = {Primary Toxoplasma gondii infection-associated with hemophagocytic syndrome in a man with HIV infection: a case report.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {35}, pmid = {34991519}, issn = {1471-2334}, support = {3110119068//the "double first-Class" university and discipline construction funds of China Medical university/ ; }, abstract = {BACKGROUND: Reactivation of latent Toxoplasma gondii (T. gondii) infection is more common than primary infection in patients with human immunodeficiency virus (HIV). We report a rare case of primary T. gondii infection-associated hemophagocytic syndrome (HPS).<br><br>CASE PRESENTATION: A man with HIV infection presented with fever, dyspnea and pancytopenia. He was diagnosed with primary T. gondii infection by the seroconversion from single-positive IgM antibody to double-positive IgM and IgG antibody. Metagenomic next-generation sequencing (mNGS) of a plasma sample yielded high reads of T. gondii DNA. He responded well to combined anti-Toxoplasma medicines and glucocorticoid treatment.<br><br>CONCLUSIONS: In patients with HPS and positive T. gondii IgM antibody, mNGS analysis of a peripheral blood sample is helpful in diagnosing disseminated T. gondii infection. The dynamic changes by serological detection for IgM and IgG of T. gondii further supported the inference that the patient has experienced a primary T. gondii infection.}, }
@article {pmid34599814, year = {2021}, author = {Lewald, KM and Abrieux, A and Wilson, DA and Lee, Y and Conner, WR and Andreazza, F and Beers, EH and Burrack, HJ and Daane, KM and Diepenbrock, L and Drummond, FA and Fanning, PD and Gaffney, MT and Hesler, SP and Ioriatti, C and Isaacs, R and Little, BA and Loeb, GM and Miller, B and Nava, DE and Rendon, D and Sial, AA and Bezerra da Silva, CS and Stockton, DG and Van Timmeren, S and Wallingford, A and Walton, VM and Wang, X and Zhao, B and Zalom, FG and Chiu, JC}, title = {Population genomics of Drosophila suzukii reveal longitudinal population structure and signals of migrations in and out of the continental United States.}, journal = {G3 (Bethesda, Md.)}, volume = {11}, number = {12}, pages = {}, pmid = {34599814}, issn = {2160-1836}, mesh = {Animals ; *Drosophila/genetics ; Fruit ; Genetic Markers ; Genomics ; *Metagenomics ; United States ; }, abstract = {Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. In this study, we sequenced whole genomes of 237 individual flies collected across the continental United States, as well as several sites in Europe, Brazil, and Asia, to identify and analyze hundreds of thousands of genetic markers. We observed strong population structure between Western and Eastern US populations, but no evidence of any population structure between different latitudes within the continental United States, suggesting that there are no broad-scale adaptations occurring in response to differences in winter climates. We detect admixture from Hawaii to the Western United States and from the Eastern United States to Europe, in agreement with previously identified introduction routes inferred from microsatellite analysis. We also detect potential signals of admixture from the Western United States back to Asia, which could have important implications for shipping and quarantine policies for exported agriculture. We anticipate this large genomic dataset will spur future research into the genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.}, }
@article {pmid34991225, year = {2022}, author = {Lee, TT and Chou, CH and Wang, C and Lu, HY and Yang, WY}, title = {Bacillus amyloliquefaciens and Saccharomyces cerevisiae feed supplements improve growth performance and gut mucosal architecture with modulations on cecal microbiota in red-feathered native chickens.}, journal = {Animal bioscience}, volume = {}, number = {}, pages = {}, doi = {10.5713/ab.21.0318}, pmid = {34991225}, issn = {2765-0189}, abstract = {Objective: The aim of study was to investigate the effects of in-feed supplementation of Bacillus amyloliquefaciens (BA) and Saccharomyces cerevisiae (SC) on growth performance, gut integrity, and microbiota modulations in red-feathered native chickens (RFCs).<br><br>Methods: A total of 18,000 RFCs in a commercial farm were evenly assigned into two dietary treatments (control diet; 0.05% BA and 0.05% SC) by randomization and raised for 11 weeks in two separate houses. Fifty RFCs in each group were randomly selected and raised in the original house with the partition for performance evaluations at the age of 9 and 11 weeks. Six non-partitioned RFCs per group were randomly selected for analyses of intestinal architecture and 16S rRNA metagenomics.<br><br>Results: Feeding BA and SC increased the body weight and body weight gain, significantly at the age of 11 weeks (p<0.05). The villus height/crypt ratio in the small intestines and Firmicutes to Bacteroidetes ratio were also notably increased (p<0.05). The supplementation did not disturb the microbial community structure but promote the featured microbial shifts characterized by the significant increments of Bernesiella, Prevotellaceae_NK3B31_group, and Butyrucimonas, following remarkable decrements of Bacteroides, Rikenellaceae_RC9_gut_group, and Succinatimonas in RFCs with growth benefits. Besides, functional pathways of peptidoglycan biosynthesis, nucleotide excision repair, glycolysis/gluconeogenesis, and aminoacyl transfer ribonucleic acid (tRNA) biosynthesis were significantly promoted (p<0.05).<br><br>Conclusion: In-feed supplementation of BA and SC enhanced the growth performance, improved mucosal architectures in small intestines, and modulated the cecal microbiota and metabolic pathways in RFCs.}, }
@article {pmid34990722, year = {2022}, author = {Wang, B and Peng, Q and Wang, R and Yu, S and Li, Q and Huang, C}, title = {Efficient Microcystis removal and sulfonamide-resistance gene propagation mitigation by constructed wetlands and functional genes analysis.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {133481}, doi = {10.1016/j.chemosphere.2021.133481}, pmid = {34990722}, issn = {1879-1298}, abstract = {Increasingly prevalent Microcystis blooms and the propagation of the associated resistance genes represent global environmental problems. Constructed wetlands (CWs) are a cost-effective technology used for wastewater treatment. In this study, the herb Alisma orientale and three industrial byproducts, namely, blast furnace slag, biochar, and sawdust, were selected to construct mini-CW units. Their potential to remediate toxic Microcystis and their influences on the behaviors of antibiotic-resistant genes (ARGs, sul1, sul2, and intl1) were analyzed. Approximately 98.46% of Microcystis cells were removed by the sawdust-based CW in just 2 d, wherein <0.37 μg/L residual microcystin (MC)-LR was detected, with a removal efficiency of >96.47%, which is potentially caused by the higher relative abundance of MC-degrading gene mlrA on the substrate. Lower target ARG accumulations in the sawdust-based CW may be attributed to the lower intl1 relative abundance and microbial function mobile element content, which could influence horizontal gene transfer. In three sequential batches for the treatment of eutrophic lake water, six sawdust-based CW units were assembled into CW microcosms. The efficiency of removal of Microcystis and MC-LR by planted CW microcosms ranged between 92.00% and 95.88% and between 86.48% and 94.82%, respectively; this was significantly (P < 0.05) higher than that by unplanted ones. Less accumulation of target ARGs was also observed in planted CWs. Planting considerably improved nitrogen removal, possibly owing to the enrichment of genes involved in the KEGG nitrogen metabolism pathway in the substrate through metagenomic analysis.}, }
@article {pmid34990038, year = {2022}, author = {Cifuentes, SG and Prado, MB and Fornasini, M and Cohen, H and Baldeón, ME and Cárdenas, PA}, title = {Saccharomyces boulardii CNCM I-745 supplementation modifies the fecal resistome during Helicobacter pylori eradication therapy.}, journal = {Helicobacter}, volume = {}, number = {}, pages = {e12870}, doi = {10.1111/hel.12870}, pmid = {34990038}, issn = {1523-5378}, support = {//Universidad San Francisco de Quito/ ; //Biocodex research grants/ ; }, abstract = {BACKGROUND: The gut microbiota is a significant reservoir of antimicrobial resistance genes (ARGs). The use and misuse of antimicrobials can select multi-resistant bacteria and modify the repertoire of ARGs in the gut. Developing effective interventions to manipulate the intestinal resistome would allow us to modify the antimicrobial resistance risk.<br><br>MATERIALS AND METHODS: Applying shotgun metagenomics, we compared the composition of fecal resistome from individuals treated with triple therapy for Helicobacter pylori plus Saccharomyces boulardii CNCM-I 745 (Sb) versus triple antibiotherapy without S. boulardii (control) before, after, and one month after treatments. DNA samples were sequenced on an Illumina NovaSeq 6000 platform. Reads were trimmed and filtered for quality, and the reads classified as host genome were removed from further analysis. We used the ResFinder database for resistome analysis and the web-based tool ResistoXplorer and RStudio for graphical representation and statistical analysis.<br><br>RESULTS: We identified 641 unique ARGs in all fecal samples, conferring resistance to 18 classes of antibiotics. The most prevalent ARGs found in at least 90% of the samples before the treatments were against tetracyclines, MLS-B (macrolide, lincosamide, and streptogramin B), beta-lactams, and aminoglycosides. Differential abundance analysis allowed the identification of ARGs significantly different between treatment groups. Thus, immediately after the treatments, the abundance of ARGs that confer resistance to lincosamides, tetracyclines, MLS-B, and two genes in the beta-lactam class (cfxA2 and cfxA3) was significantly lower in the group that received Sb than in the control group (edgeR, FDR <0.05).<br><br>CONCLUSION: Our study demonstrated that the addition of S. boulardii CNCM-I 745 to the conventional antibiotic eradication therapy for H. pylori reduced the abundance of ARGs, particularly those genes that confer resistance to lincosamides, tetracyclines, MLS-B, and a few genes in the beta-lactams class.}, }
@article {pmid34989986, year = {2022}, author = {Philips, CA and Augustine, P and Ganesan, K and Ranade, S and Chopra, V and Patil, K and Shende, S and Ahamed, R and Kumbar, S and Rajesh, S and George, T and Mohanan, M and Mohan, N and Phadke, N and Rani, M and Narayanan, A and Jagan, SM}, title = {The role of gut microbiota in clinical complications, disease severity, and treatment response in severe alcoholic hepatitis.}, journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology}, volume = {}, number = {}, pages = {}, pmid = {34989986}, issn = {0975-0711}, abstract = {BACKGROUND: Dysbiotic gut bacteria engage in the development and progression of severe alcoholic hepatitis (SAH). We aimed to characterize bacterial communities associated with clinical events (CE), identify significant bacteria linked to CE, and define bacterial relationships associated with specific CE and outcomes at baseline and after treatment in SAH.<br><br>METHODS: We performed 16-s rRNA sequencing on stool samples (n=38) collected at admission and the last follow-up within 90 days in SAH patients (n=26; 12 corticosteroids; 14 granulocyte colony-stimulating factor, [G-CSF]). Validated pipelines were used to plot bacterial communities, profile functional metabolism, and identify significant taxa and functional metabolites. Conet/NetworkX® was utilized to identify significant non-random patterns of bacterial co-presence and mutual exclusion for clinical events.<br><br>RESULTS: All the patients were males with median discriminant function (DF) 64, Child-Turcotte-Pugh (CTP) 12, and model for end-stage liver disease (MELD) score 25.5. At admission, 27%, 42%, and 58% had acute kidney injury (AKI), hepatic encephalopathy (HE), and infections respectively; 38.5% died at end of follow-up. Specific bacterial families were associated with HE, sepsis, disease severity, and death. Lachnobacterium and Catenibacterium were associated with HE, and Pediococcus with death after steroid treatment. Change from Enterococcus (promotes AH) to Barnesiella (inhibits E. faecium) was significant after G-CSF. Phenylpropanoid-biosynthesis (innate-immunity) and glycerophospholipid-metabolism (cellular-integrity) pathways in those without infections and the death, respectively, were upregulated. Mutual interactions between Enterococcus cecorum, Acinetobacter schindleri, and Mitsuokella correlated with admission AKI.<br><br>CONCLUSIONS: Specific gut microbiota, their interactions, and metabolites are associated with complications of SAH and treatment outcomes. Microbiota-based precision medicine as adjuvant treatment may be a new therapeutic area.}, }
@article {pmid34989623, year = {2022}, author = {Kaszab, E and Laczkó, L and Bali, K and Fidrus, E and Bányai, K and Kardos, G}, title = {Draft Genome Sequences of Lacticaseibacillus rhamnosus cek-R1, Lacticaseibacillus paracasei cek-R2, and Lentilactobacillus otakiensis cek-R3, Isolated from a Beetroot Product.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0092121}, doi = {10.1128/MRA.00921-21}, pmid = {34989623}, issn = {2576-098X}, abstract = {Lactic acid bacteria (LAB) participate in fermentation processes and have probiotic potential. The genomes of three LAB strains, Lacticaseibacillus rhamnosus cek-R1, Lacticaseibacillus paracasei subsp. paracasei cek-R2, and Lentilactobacillus otakiensis cek-R3, isolated from a beetroot product, were characterized. The results contribute to our understanding of the beneficial properties of LAB.}, }
@article {pmid34989619, year = {2022}, author = {Bogoyavlenskiy, A and Alexyuk, M and Alexyuk, P and Amanbayeva, M and Anarkulova, E and Imangazy, A and Bektuganova, A and Berezin, V}, title = {Metagenomic Exploration of Koumiss from Kazakhstan.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0108221}, doi = {10.1128/mra.01082-21}, pmid = {34989619}, issn = {2576-098X}, abstract = {Here, we report a metagenomic analysis of koumiss from Kazakhstan. In this study, shotgun metagenomic sequencing of the RNA and DNA viral community was performed.}, }
@article {pmid34989610, year = {2022}, author = {Vecherskii, MV and Khayrullin, DR and Shadrin, AM and Lisov, AV and Zavarzina, AG and Zavarzin, AA and Leontievsky, AA}, title = {Metagenomes of Lichens Solorina crocea and Peltigera canina.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0100021}, doi = {10.1128/MRA.01000-21}, pmid = {34989610}, issn = {2576-098X}, abstract = {Lichen genomes are usually considered genomes of separately cultured mycobiont and photobiont. Analysis of lichen metagenomes can give important information on specific lichen-associated microorganisms that can affect lichen metabolism. Here, we report a metagenome of peltigeralean lichens, containing cyanobacterial (Peltigera canina) and cyanobacterial/green algal (Solorina crocea) partners.}, }
@article {pmid34989406, year = {2022}, author = {Ferravante, C and Sanna, G and Melone, V and Fromentier, A and Rocco, T and D'Agostino, Y and Lamberti, J and Alexandrova, E and Pecoraro, G and Pagliano, P and Astorri, R and Manzin, A and Weisz, A and Giurato, G and Galdiero, M and Rizzo, F and Franci, G}, title = {Nasopharyngeal virome analysis of COVID-19 patients during three different waves in Campania Region of Italy.}, journal = {Journal of medical virology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jmv.27571}, pmid = {34989406}, issn = {1096-9071}, abstract = {From December 2019, SARS-CoV-2 infection has spread rapidly, leading to a global pandemic. Little is known about possible relationships between SARS-CoV-2 and other viruses in the respiratory system affecting patient prognosis and outcomes. This study aims to characterize respiratory virome profiles in association with SARS-CoV-2 infection and disease severity, through the analysis in 89 nasopharyngeal swabs collected in apatient's cohort from the Campania region (Southern Italy). Results show coinfections with viral species belonging to Coronaviridae, Retroviridae, Herpesviridae, Poxviridae, Pneumoviridae, Pandoraviridae, and Anelloviridae families and only 2% of the cases (2/89) identified respiratory viruses. This article is protected by copyright. All rights reserved.}, }
@article {pmid34988184, year = {2021}, author = {Gao, D and Hu, Y and Jiang, X and Pu, H and Guo, Z and Zhang, Y}, title = {Applying the pathogen-targeted next-generation sequencing method to pathogen identification in cerebrospinal fluid.}, journal = {Annals of translational medicine}, volume = {9}, number = {22}, pages = {1675}, doi = {10.21037/atm-21-5488}, pmid = {34988184}, issn = {2305-5839}, abstract = {Background: The cerebrospinal fluid (CSF) culture is a widely used method for the diagnosis of meningitis, but its detection sensitivity is low. Several new methods have been developed for pathogen detection, including metagenomic next-generation sequencing (mNGS) and pathogen-targeted NGS (ptNGS). In this study, we aimed to evaluate the performance of ptNGS in pathogen detection in CSF.<br><br>Methods: CSF specimens were acquired from 38 patients with meningitis who were diagnosed at Xuanwu Hospital, Capital Medical University between October 2020 and February 2021. DNA was extracted from the CSF samples, and pathogens were identified using both ptNGS and mNGS. SPSS 22.0 software was used to compare the pathogen detection performance of ptNGS and mNGS in CSF.<br><br>Results: Among the 38 patients with meningitis, 14 had a non-infectious disease (NID) and 24 had an infectious disease (ID). Of the 38 samples, both ptNGS and mNGS detected 9 (23.7%) positive samples, and 12 (31.6%) negative samples. Thirteen (34.2%) samples were detected to be positive by ptNGS only, and 4 (10.5%) were detected to be positive by mNGS only. The positivity rate detected by ptNGS for the ID group was higher than that detected by mNGS (P=0.080), and the positivity rates detected by ptNGS and mNGS for the NID group were comparable. The positive predictive value (PPV) and negative predictive value (NPV) of diagnosing an ID by ptNGS were 77.3% and 56.3%, respectively. While, the PPV and NPV of diagnosing an ID by mNGS were 76.9% and 44.0%, respectively. ptNGS increased the sensitivity rate by approximately 70%. The sensitivity rate of ptNGS was higher than that of mNGS (70.8% vs. 41.7%), while the specificity rate of mNGS was higher than that of ptNGS (78.6% vs. 64.3%). Additionally, ptNGS required a shorter time for pathogen diagnosis (15 vs. 24 hrs) and had lower costs than mNGS.<br><br>Conclusions: ptNGS has a number of advantages over mNGS, including its sensitivity, timeliness, and economy, all factors that are important considerations in clinical use.}, }
@article {pmid34987633, year = {2022}, author = {Png, CW and Lee, WJJ and Chua, SJ and Zhu, F and ,  and Yeoh, KG and Zhang, Y}, title = {Mucosal microbiome associates with progression to gastric cancer.}, journal = {Theranostics}, volume = {12}, number = {1}, pages = {48-58}, doi = {10.7150/thno.65302}, pmid = {34987633}, issn = {1838-7640}, abstract = {Background &amp; Aims: Dysbiosis is associated with gastric cancer (GC) development. However, no longitudinal study was carried out to identify key bacteria that could predict for GC progression. Here, we aimed to investigate changes in bacterial metagenome prior to GC and develop a microbiome-based predictive model to accurately classify patients at risk of GC. Methods: Bacterial 16S rDNA was sequenced from 89 gastric antral biopsies obtained from 43 participants. This study was nested in a prospective, longitudinal study, whereby study participants underwent screening gastroscopy, with further 1-2 yearly surveillance gastroscopies for at least 5 years. Putative bacterial taxonomic and functional features associated with GC carcinogenesis were identified by comparing between controls, patients with gastric intestinal metaplasia (IM) and patients with early gastric neoplasia (EGN). Results: Patients with EGN had enrichment of Proteobacteria (in particular Proteus genus) and depletion of Bacteroidetes (in particular S24-7 family) in their gastric mucosa. Sequencing identified more patients with Helicobacter pylori compared to histopathological assessment, while H. pylori was also significantly enriched in EGN. Furthermore, a total of 261 functional features, attributing to 97 KEGG pathways were differentially abundant at baseline between patients who subsequent developed EGN (n = 13/39) and those who did not. At the same time, a constellation of six microbial taxonomic features present at baseline, provided the highest classifying power for subsequent EGN (AUC = 0.82). Conclusion: Our study highlights early microbial changes associated with GC carcinogenesis, suggesting a potential role for prospective microbiome surveillance for GC.}, }
@article {pmid34987487, year = {2021}, author = {Asare, PT and Greppi, A and Pennacchia, A and Brenig, K and Geirnaert, A and Schwab, C and Stephan, R and Lacroix, C}, title = {In vitro Modeling of Chicken Cecal Microbiota Ecology and Metabolism Using the PolyFermS Platform.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {780092}, doi = {10.3389/fmicb.2021.780092}, pmid = {34987487}, issn = {1664-302X}, abstract = {Continuous in vitro fermentation models provide a useful tool for a fast, reproducible, and direct assessment of treatment-related changes in microbiota metabolism and composition independent of the host. In this study, we used the PolyFermS model to mimic the conditions of the chicken cecum and evaluated three nutritive media for in vitro modeling of the chicken cecal microbiota ecology and metabolism. We observed that our model inoculated with immobilized cecal microbiota and fed with a modified Viande Levure medium (mVL-3) reached a high bacterial cell density of up to approximately 10.5 log cells per mL and stable microbiota composition, akin to the host, during 82 days of continuous operation. Relevant bacterial functional groups containing primary fibrolytic (Bacteroides, Bifidobacteriaceae, Ruminococcaceae), glycolytic (Enterococcus), mucolytic (Bacteroides), proteolytic (Bacteroides), and secondary acetate-utilizing butyrate-producing and propionate-producing (Lachnospiraceae) taxa were preserved in vitro. Besides, conserved metabolic and functional Kyoto Encyclopedia of Genes and Genomes pathways were observed between in vitro microbiota and cecal inoculum microbiota as predicted by functional metagenomics analysis. Furthermore, we demonstrated that the continuous inoculation provided by the inoculum reactor generated reproducible metabolic profiles in second-stage reactors comparable to the chicken cecum, allowing for the simultaneous investigation and direct comparison of different treatments with a control. In conclusion, we showed that PolyFermS is a suitable model for mimicking chicken cecal microbiota fermentation allowing ethical and ex vivo screening of environmental factors, such as dietary additives, on chicken cecal fermentation. We report here for the first time a fermentation medium (mVL-3) that closely mimics the substrate conditions in the chicken cecum and supports the growth and metabolic activity of the cecal bacterial akin to the host. Our PolyFermS chicken cecum model is a useful tool to study microbiota functionality and structure ex vivo.}, }
@article {pmid34987055, year = {2022}, author = {Joseph, TA and Chlenski, P and Litman, A and Korem, T and Pe'er, I}, title = {Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.275533.121}, pmid = {34987055}, issn = {1549-5469}, abstract = {Patterns of sequencing coverage along a bacterial genome---summarized by a peak-to-trough ratio (PTR)---have been shown to accurately reflect microbial growth rates, revealing a new facet of microbial dynamics and host-microbe interactions. Here, we introduce CoPTR (Compute PTR): a tool for computing PTRs from complete reference genomes and assemblies. Using simulations and data from growth experiments in simple and complex communities, we show that CoPTR is more accurate than the current state-of-the-art, while also providing more PTR estimates overall. We further develop theory formalizing a biological interpretation for PTRs. Using a reference database of 2935 species, we applied CoPTR to a case-control study of 1304 metagenomic samples from 106 individuals with inflammatory bowel disease. We show that growth rates are personalized, are only loosely correlated with relative abundances, and are associated with disease status. We conclude by demonstrating how PTRs can be combined with relative abundances and metabolomics to investigate their effect on the microbiome.}, }
@article {pmid34986625, year = {2022}, author = {Sun, HY and Li, B and Liu, Y and You, HL and Liu, YF}, title = {[Clinical analysis of 3 cases of mucormycosis in children with acute lymphoblastic leukemia and literature review].}, journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics}, volume = {60}, number = {1}, pages = {56-61}, doi = {10.3760/cma.j.cn112140-20210711-00571}, pmid = {34986625}, issn = {0578-1310}, abstract = {Objective: To investigate the clinical features, diagnosis,treatment and prognosis of children with acute lymphoblastic leukemia complicated with mucormycosis, and to improve the understanding of the disease. Methods: The clinical data of 3 children with acute lymphoblastic leukemia (ALL) complicated with mucormycosis treated at the First Affiliated Hospital of Zhengzhou University between October 2020 and January 2021 were analyzed retrospectively. Literature search and review covered the China national knowledge infrastructure, Wanfang database and Pubmed using the keywords of "acute lymphoblastic leukemia" and "mucormycosis" up to June 2021. Results: Case 1, a 12-year-old boy, was diagnosed with ALL, developed fever and chest pain during induction therapy. The Metagenomic next-generation sequencing (mNGS) testing of alveolar perfusion fluid suggested infection with Rhizopus oryzae. Amphotericin B combined with posaconazole was applied and amphotericin B was removed after improvement. Bone destruction was indicated by CT. Amphotericin B was applied again. Case 2, a 4-year-old boy, with a history of pallor and tetter, was diagnosed with ALL. He developed cough and fever during induction therapy. mNGS of blood suggested infection with Rhizomucor pusillus. Amphotericin B combined with voriconazole was applied, but the situation was not significantly improved. The disseminated infection occurred. Amphotericin B combined with posaconazole was applied and vacuum sealing drainage was performed. Case 3, a 2-year-old girl, was diagnosed with ALL, developed fever and cough during induction therapy. Rhizomucor pusillus was indicated by mNGS. Amphotericin B combined with posaconazole was used, and posaconazole was stopped after improvement. Follow-up until June 2021, the condition of the 3 children improved. There was no recurrent Mucor infection, and the primary hematopathy was in complete remission. According to the literature, 7 reports were found in Chinese journals, while 17 reports were found in English literature, 25 cases have been reported. Among a total of 28 children, 11 cases rhino-orbito-cerebral mucormycosis, four pulmonary mucormycosis, 2 cutaneous mucormycosis, 2 gastrointestinal mucormycosis and 9 disseminated mucormycosis. There were 17 cases developed infection during induction chemotherapy, 8 cases during maintenance therapy, 3 cases after hematopoietic stem cell transplantation. Voriconazole was used in 15 cases; 19 cases were treated with combined surgery, 7 cases were treated with drugs only, 2 cases were untreated; 21 cases showed improvement after treatment. Death occurred in seven cases. Conclusions: ALL complicated with mucormycosis often occurs in the stage of induction therapy. The clinical features lacked specificity, mNGS can help find the pathogen and provide evidence for diagnosis. Surgical treatment also could be combined when necessary, which is helpful to improve the prognosis.}, }
@article {pmid34986574, year = {2022}, author = {Liu, Y and Neal, AL and Zhang, X and Fan, H and Liu, H and Li, Z}, title = {Cropping system exerts stronger influence on antibiotic resistance gene assemblages in greenhouse soils than reclaimed wastewater irrigation.}, journal = {Journal of hazardous materials}, volume = {425}, number = {}, pages = {128046}, doi = {10.1016/j.jhazmat.2021.128046}, pmid = {34986574}, issn = {1873-3336}, abstract = {The effects of reclaimed wastewater (RW) irrigation on the spread of antibiotic resistance genes (ARGs) in soil is modulated by a myriad of biotic and abiotic factors and their relative significance remains vague. We compared microbial communities, assemblages of genes associated with microbial resistance to antibiotics, biocides and metals, and insertion sequences (ISs) in soils following 16 years of irrigation with groundwater (GW), RW or alternately with GW and RW in two greenhouses with different cropping systems, using shotgun metagenome sequencing. The results showed that cropping system exerted greater influence than irrigation on the profile of ISs and resistance genes. This influence was most strongly associated with concentrations of copper, mercury and perfloxacin in the soils. There was no significant difference in soil ARG profiles between continuous RW irrigation and alternating GW and RW irrigation. Proteobacteria, Actinobacteria and Firmicutes and a limited number of ISs were closely associated with the detected ARGs. Most ARGs were found to co-occur with metal and biocide resistance genes through the mechanism of efflux pumps. These findings highlight the significance of understanding and improving crop management in mitigating the dissemination of ARGs in soils irrigated with RW.}, }
@article {pmid34856363, year = {2022}, author = {Morikawa, A and Kawabata, A and Shirahige, K and Akiyama, T and Okamoto, A and Sutani, T}, title = {Altered cervicovaginal microbiota in premenopausal ovarian cancer patients.}, journal = {Gene}, volume = {811}, number = {}, pages = {146083}, doi = {10.1016/j.gene.2021.146083}, pmid = {34856363}, issn = {1879-0038}, mesh = {Adult ; Aged ; Aged, 80 and over ; Bacterial Typing Techniques/methods ; Biomarkers ; Carcinoma, Ovarian Epithelial/*microbiology ; Case-Control Studies ; Cervix Uteri/*microbiology ; DNA, Bacterial ; Female ; Humans ; Japan ; Lactobacillus/classification/genetics ; Metagenome ; *Microbiota ; Middle Aged ; Ovarian Neoplasms/*microbiology ; Postmenopause ; Premenopause ; RNA, Ribosomal, 16S ; Vagina/*microbiology ; Young Adult ; }, abstract = {Nearly three hundred thousand female patients are diagnosed with ovarian cancer in the world annually, and this number shows an increasing trend. However, characteristic symptoms caused by ovarian cancer are so few that early diagnosis remains challenging, and an effective screening method has not yet been established. Here, we conducted a case-control study in Japan to analyze the association between cervicovaginal microbiome and ovarian cancer, using 16S rRNA amplicon sequencing. Analysis of DNA extracted from cervical smear samples revealed Lactobacillus-dominant and Lactobacillus-deficient, highly-diversified bacterial communities in premenopausal and postmenopausal healthy controls, respectively, as reported for vaginal microbiota previously. We found that cervicovaginal microbiota in ovarian cancer patients, regardless of their menopausal status, were frequently a diversified community and similar to those in healthy subjects at postmenopausal ages. The diverse microbiota was associated with the major histotypes of epithelial ovarian cancer, including serous ovarian cancer and ovarian clear cell cancer. The present study implies the potential of a cervicovaginal microbiome biomarker in screening ovarian cancer in premenopausal women.}, }
@article {pmid34354062, year = {2021}, author = {Schaan, AP and Sarquis, D and Cavalcante, GC and Magalhães, L and Sacuena, ERP and Costa, J and Fonseca, D and Mello, VJ and Guerreiro, JF and Ribeiro-Dos-Santos, Â}, title = {The structure of Brazilian Amazonian gut microbiomes in the process of urbanisation.}, journal = {NPJ biofilms and microbiomes}, volume = {7}, number = {1}, pages = {65}, pmid = {34354062}, issn = {2055-5008}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Brazil ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Life Style ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rural Population ; Urban Population ; *Urbanization ; }, abstract = {Shifts in subsistence strategy among Native American people of the Amazon may be the cause of typically western diseases previously linked to modifications of gut microbial communities. Here, we used 16S ribosomal RNA sequencing to characterise the gut microbiome of 114 rural individuals, namely Xikrin, Suruí and Tupaiú, and urban individuals from Belém city, in the Brazilian Amazon. Our findings show the degree of potential urbanisation occurring in the gut microbiome of rural Amazonian communities characterised by the gradual loss and substitution of taxa associated with rural lifestyles, such as Treponema. Comparisons to worldwide populations indicated that Native American groups are similar to South American agricultural societies and urban groups are comparable to African urban and semi-urban populations. The transitioning profile observed among traditional populations is concerning in light of increasingly urban lifestyles. Lastly, we propose the term "tropical urban" to classify the microbiome of urban populations living in tropical zones.}, }
@article {pmid34986419, year = {2022}, author = {Ariaeenejad, S and Kavousi, K and Mamaghani, ASA and Ghasemitabesh, R and Salekdeh, GH}, title = {Simultaneous hydrolysis of various protein-rich industrial wastes by a naturally evolved protease from tannery wastewater microbiota.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152796}, doi = {10.1016/j.scitotenv.2021.152796}, pmid = {34986419}, issn = {1879-1026}, abstract = {Elimination of protein-rich waste materials is one of the vital environmental protection requirements. Using of non-naturally occurring chemicals for their remediation properties can potentially induce new pollutants. Therefore, enzymes encoded in the genomes of microorganisms evolved in the same environment can be considered suitable alternatives to chemicals. Identification of efficient proteases that can hydrolyze recalcitrant, protein-rich wastes produced by various industrial processes has been widely welcomed as an eco-friendly waste management strategy. In this direction, we attempted to screen a thermo-halo-alkali-stable metagenome-derived protease (PersiProtease1) from tannery wastewater. The PersiProtease1 exhibited high pH stability over a wide range and at 1 h in pH 11.0 maintained 87.59% activity. The enzyme possessed high thermal stability while retaining 76.64% activity after 1 h at 90 °C. Moreover, 65.34% of the initial activity of the enzyme remained in the presence of 6 M NaCl, showing tolerance against high salinity. The presence of various metal ions, inhibitors, and organic solvents did not remarkably inhibit the activity of the discovered protease. The PersiProtease1 was extracted from the tannery wastewater microbiota and efficiently applied for biodegradation of real sample tannery wastewater protein, chicken feathers, whey protein, dehairing sheepskins, and waste X-ray films. PersiProtease1 proved its enormous potential in simultaneous biodegradation of solid and liquid protein-rich industrial wastes based on the results.}, }
@article {pmid34986353, year = {2022}, author = {Yan, S and Conley, JM and Reilly, AM and Stull, ND and Abhyankar, SD and Ericsson, AC and Kono, T and Molosh, AI and Kubal, CA and Evans-Molina, C and Ren, H}, title = {Intestinal Gpr17 deficiency improves glucose metabolism by promoting GLP-1 secretion.}, journal = {Cell reports}, volume = {38}, number = {1}, pages = {110179}, doi = {10.1016/j.celrep.2021.110179}, pmid = {34986353}, issn = {2211-1247}, abstract = {G protein-coupled receptors (GPCRs) in intestinal enteroendocrine cells (EECs) respond to nutritional, neural, and microbial cues and modulate the release of gut hormones. Here we show that Gpr17, an orphan GPCR, is co-expressed in glucagon-like peptide-1 (GLP-1)-expressing EECs in human and rodent intestinal epithelium. Acute genetic ablation of Gpr17 in intestinal epithelium improves glucose tolerance and glucose-stimulated insulin secretion (GSIS). Importantly, inducible knockout (iKO) mice and Gpr17 null intestinal organoids respond to glucose or lipid ingestion with increased secretion of GLP-1, but not the other incretin glucose-dependent insulinotropic polypeptide (GIP). In an in vitro EEC model, overexpression or agonism of Gpr17 reduces voltage-gated calcium currents and decreases cyclic AMP (cAMP) production, and these are two critical factors regulating GLP-1 secretion. Together, our work shows that intestinal Gpr17 signaling functions as an inhibitory pathway for GLP-1 secretion in EECs, suggesting intestinal GPR17 is a potential target for diabetes and obesity intervention.}, }
@article {pmid34986315, year = {2022}, author = {Mejia, ME and Ottinger, S and Vrbanac, A and Babu, P and Zulk, JJ and Moorshead, D and Bode, L and Nizet, V and Patras, KA}, title = {Human Milk Oligosaccharides Reduce Murine Group B Streptococcus Vaginal Colonization with Minimal Impact on the Vaginal Microbiota.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0088521}, doi = {10.1128/msphere.00885-21}, pmid = {34986315}, issn = {2379-5042}, abstract = {Group B Streptococcus (GBS) colonizes the vaginal mucosa of a significant percentage of healthy women and is a leading cause of neonatal bacterial infections. Currently, pregnant women are screened in the last month of pregnancy, and GBS-positive women are given antibiotics during parturition to prevent bacterial transmission to the neonate. Recently, human milk oligosaccharides (HMOs) isolated from breastmilk were found to inhibit GBS growth and biofilm formation in vitro, and women that make certain HMOs are less likely to be vaginally colonized with GBS. Using in vitro human vaginal epithelial cells and a murine vaginal colonization model, we tested the impact of HMO treatment on GBS burdens and the composition of the endogenous microbiota by 16S rRNA amplicon sequencing. HMO treatment reduced GBS vaginal burdens in vivo with minimal alterations to the vaginal microbiota. HMOs displayed potent inhibitory activity against GBS in vitro, but HMO pretreatment did not alter adherence of GBS or the probiotic Lactobacillus rhamnosus to human vaginal epithelial cells. In addition, disruption of a putative GBS glycosyltransferase (Δsan_0913) rendered the bacterium largely resistant to HMO inhibition in vitro and in vivo but did not compromise its adherence, colonization, or biofilm formation in the absence of HMOs. We conclude that HMOs are a promising therapeutic bioactive to limit GBS vaginal colonization with minimal impacts on the vaginal microenvironment. IMPORTANCE During pregnancy, GBS ascension into the uterus can cause fetal infection or preterm birth. In addition, GBS exposure during labor creates a risk of serious disease in the vulnerable newborn and mother postpartum. Current recommended prophylaxis consists of administering broad-spectrum antibiotics to GBS-positive mothers during labor. Although antibiotics have significantly reduced GBS neonatal disease, there are several unintended consequences, including altered neonatal gut bacteria and increased risk for other types of infection. Innovative preventions displaying more targeted antimicrobial activity, while leaving the maternal microbiota intact, are thus appealing. Using a mouse model, we found that human milk oligosaccharides (HMOs) reduce GBS burdens without perturbing the vaginal microbiota. We conclude that HMOs are a promising alternative to antibiotics to reduce GBS neonatal disease.}, }
@article {pmid34986232, year = {2021}, author = {Essack, S}, title = {BSAC Vanguard Series: From treatment options to precision medicine: the future of 'omics-based' antibiotic resistance surveillance data.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {77}, number = {1}, pages = {5-6}, doi = {10.1093/jac/dkab417}, pmid = {34986232}, issn = {1460-2091}, abstract = {Conventional culture-based phenotypic and genomic surveillance has drawbacks and may not necessarily reflect the true burden of antibiotic resistance. The integration of metagenomic surveillance with transcriptomics and proteomics will yield a step change in the utility of surveillance data from treatment options to precision medicine.}, }
@article {pmid34985651, year = {2022}, author = {Szychowiak, P and Villageois-Tran, K and Patrier, J and Timsit, JF and Ruppé, É}, title = {The role of the microbiota in the management of intensive care patients.}, journal = {Annals of intensive care}, volume = {12}, number = {1}, pages = {3}, pmid = {34985651}, issn = {2110-5820}, abstract = {The composition of the gut microbiota is highly dynamic and changes according to various conditions. The gut microbiota mainly includes difficult-to-cultivate anaerobic bacteria, hence knowledge about its composition has significantly arisen from culture-independent methods based on next-generation sequencing (NGS) such as 16S profiling and shotgun metagenomics. The gut microbiota of patients hospitalized in intensive care units (ICU) undergoes many alterations because of critical illness, antibiotics, and other ICU-specific medications. It is then characterized by lower richness and diversity, and dominated by opportunistic pathogens such as Clostridioides difficile and multidrug-resistant bacteria. These alterations are associated with an increased risk of infectious complications or death. Specifically, at the time of writing, it appears possible to identify distinct microbiota patterns associated with severity or infectivity in COVID-19 patients, paving the way for the potential use of dysbiosis markers to predict patient outcomes. Correcting the microbiota disturbances to avoid their consequences is now possible. Fecal microbiota transplantation is recommended in recurrent C. difficile infections and microbiota-protecting treatments such as antibiotic inactivators are currently being developed. The growing interest in the microbiota and microbiota-associated therapies suggests that the control of the dysbiosis could be a key factor in the management of critically ill patients. The present narrative review aims to provide a synthetic overview of microbiota, from healthy individuals to critically ill patients. After an introduction to the different techniques used for studying the microbiota, we review the determinants involved in the alteration of the microbiota in ICU patients and the latter's consequences. Last, we assess the means to prevent or correct microbiota alteration.}, }
@article {pmid34985131, year = {2022}, author = {Monaco, AP}, title = {The selfish environment meets the selfish gene: Coevolution and inheritance of RNA and DNA pools: A model for organismal life incorporating coevolution, horizontal transfer, and inheritance of internal and external RNA and DNA pools.: A model for organismal life incorporating coevolution, horizontal transfer, and inheritance of internal and external RNA and DNA pools.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2100239}, doi = {10.1002/bies.202100239}, pmid = {34985131}, issn = {1521-1878}, abstract = {Throughout evolution, there has been interaction and exchange between RNA pools in the environment, and DNA and RNA pools of eukaryotic organisms. Metagenomic and metatranscriptomic sequencing of invertebrate hosts and their microbiota has revealed a rich evolutionary history of RNA virus shuttling between species. Horizontal transfer adapted the RNA pool for successful future interactions which lead to zoonotic transmission and detrimental RNA viral pandemics like SARS-CoV2. In eukaryotes, noncoding RNA (ncRNA) is an established mechanism derived from prokaryotes to defend against viral attack through innate immunity and regulation of host-derived mRNA. Transgenerational inheritance of ncRNA is evidence for feedforward adaptive immunity and epigenetically encoded environmental change across generations, which may explain the ''missing heritability'' of common disease. Causal graph theory and the Price Equation can model epigenetic inheritance involving dynamic internal and external RNA pools. Experimental designs should include metatranscriptomic analyses to understand how ncRNA responds to rapidly changing environmental conditions, within and between organisms, and across generations.}, }
@article {pmid34984789, year = {2022}, author = {Chazan, A and Rozenberg, A and Mannen, K and Nagata, T and Tahan, R and Yaish, S and Larom, S and Inoue, K and Béjà, O and Pushkarev, A}, title = {Diverse heliorhodopsins detected via functional metagenomics in freshwater Actinobacteria, Chloroflexi and Archaea.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15890}, pmid = {34984789}, issn = {1462-2920}, support = {3592/19//Israel Science Foundation/ ; JPMJPR1888//Japan Science and Technology Agency/ ; 17H03007//Japan Society for the Promotion of Science London/ ; 20K21383//Japan Society for the Promotion of Science London/ ; }, abstract = {The recently discovered rhodopsin family of heliorhodopsins (HeRs) is abundant in diverse microbial environments. So far, the functional and biological roles of HeRs remain unknown. To tackle this issue, we combined experimental and computational screens to gain some novel insights. Here, 10 readily expressed HeR genes were found using functional metagenomics on samples from two freshwater environments. These HeRs originated from diverse prokaryotic groups: Actinobacteria, Chloroflexi and Archaea. Heterologously expressed HeRs absorbed light in the green and yellow wavelengths (543-562 nm) and their photocycles exhibited diverse kinetic characteristics. To approach the physiological function of the HeRs, we used our environmental clones along with thousands of microbial genomes to analyze genes neighbouring HeRs. The strongest association was found with the DegV family involved in activation of fatty acids, which allowed us to hypothesize that HeRs might be involved in light-induced membrane lipid modifications.}, }
@article {pmid34984661, year = {2022}, author = {Bocatti, CR and Ferreira, E and Ribeiro, RA and de Oliveira Chueire, LM and Delamuta, JRM and Kobayashi, RKT and Hungria, M and Nogueira, MA}, title = {Microbiological quality analysis of inoculants based on Bradyrhizobium spp. and Azospirillum brasilense produced "on farm" reveals high contamination with non-target microorganisms.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {34984661}, issn = {1678-4405}, support = {CNPq 465133/2014-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Fundação Aaucária-STI 043/2019//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CAPES//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 433656/2018-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {The use of inoculants carrying diazotrophic and other plant growth-promoting bacteria plays an essential role in the Brazilian agriculture, with a growing use of microorganism-based bioproducts. However, in the last few years, some farmers have multiplied microorganisms in the farm, known as "on farm" production, including inoculants of Bradyrhizobium spp. for soybean (Glycine max L. Merrill.) and Azospirillum brasilense for corn (Zea mays L.) or co-inoculation in soybean. The objective was to assess the microbiological quality of such inoculants concerning the target microorganisms and contaminants. In the laboratory, 18 samples taken in five states were serial diluted and spread on culture media for obtaining pure and morphologically distinct colonies of bacteria, totaling 85 isolates. Molecular analysis based on partial sequencing of the 16S rRNA gene revealed 25 genera of which 44% harbor species potentially pathogenic to humans; only one of the isolates was identified as Azospirillum brasilense, whereas no isolate was identified as Bradyrhizobium. Among 34 isolates belonging to genera harboring species potentially pathogenic to humans, 12 had no resistance to antibiotics, six presented intrinsic resistance, and 18 presented non-intrinsic resistance to at least one antibiotic. One of the samples analyzed with a shotgun-based metagenomics approach to check for the microbial diversity showed several genera of microorganisms, mainly Acetobacter (~ 32% of sequences) but not the target microorganism. The samples of inoculants produced on farm were highly contaminated with non-target microorganisms, some of them carrying multiple resistances to antibiotics.}, }
@article {pmid34984487, year = {2022}, author = {He, Q and Zhang, Y and Ma, D and Zhang, W and Zhang, H}, title = {Lactobacillus casei Zhang exerts anti-obesity effect to obese glut1 and gut-specific-glut1 knockout mice via gut microbiota modulation mediated different metagenomic pathways.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, pmid = {34984487}, issn = {1436-6215}, support = {31720103911//national natural science foundation of china/ ; 31972083//national natural science foundation of china/ ; 32001711//national natural science foundation of china/ ; }, abstract = {PURPOSE: Obesity is a major risk factor for various metabolic diseases, including metabolic syndrome and type-2 diabetes. Glucose transporter 1 (GLUT1) impairment has been proposed as a mechanism of fat accumulation and glucose tolerance. Our aims were to determine the role of intestinal epithelial glut1 activity in obesity and the mechanism of anti-obesity effect of Lactobacillus casei Zhang (LCZ) intervention in the absence of gut villi-specific glut1 expression.<br><br>METHODS: This study compared the body weight, intestinal microbiota perturbations, fat mass accumulation, and glucose tolerance (by oral glucose tolerance test) between high-fat diet fed villi-specific glut1 knockout (KO) mice and control mice (glut1 flox/flox) with/without LCZ intervention. The intestinal microbiota was evaluated by metagenomic sequencing.<br><br>RESULTS: Our results showed that villi-specific glut1 KO mice had more fat deposition at the premetaphase stage, impaired glucose tolerance, and obvious alterations in gut microbiota compared to control mice. Probiotic administration significantly lowered the body weight, the weights of mesenteric and perirenal white adipose tissues (WAT), and mediated gut microbiota modulation in both types of KO and control mice. The species Barnesiella intestinihominis and Faecalibaculum rodentium might contribute to fasting fat mass accumulation associated with gut-specific glut1 inactivation, while the probiotic-mediated anti-obesity effect was linked to members of the Bacteroides genera, Odoribacter genera and Alistipes finegoldii.<br><br>CONCLUSION: Our study demonstrated that abrogating gut epithelial GLUT1 activity affected the gut microbiota, fat mass accumulation, and glucose tolerance; and LCZ administration reduced fat mass accumulation and central obesity.}, }
@article {pmid34984011, year = {2021}, author = {Katagiri, M and Kuroda, M and Sekizuka, T and Nakada, N and Ito, Y and Otsuka, M and Watanabe, M and Kusachi, S}, title = {Comprehensive Genomic Survey of Antimicrobial-Resistance Bacteria in the Sewage Tank Replacement with Hospital Relocation.}, journal = {Infection and drug resistance}, volume = {14}, number = {}, pages = {5563-5574}, doi = {10.2147/IDR.S336418}, pmid = {34984011}, issn = {1178-6973}, abstract = {Background: Excrement containing antimicrobial-resistant bacteria (ARB) is discharged from the hospital sewage through wastewater treatment plants (WWTP) into rivers, increasing the antimicrobial resistance (AMR) burden on the environment.<br><br>Purpose: We illustrate the contamination of hospital sewage tanks with ARB harboring antimicrobial resistance genes (ARGs) using comprehensive metagenomic sequencing. During the study period, we moved to a new hospital building constructed for renovation. Therefore, we investigated the difference in bacterial flora in the sewage tanks for each building with different departments, and the change in bacterial flora over time in new sewage tanks. Furthermore, we performed a comparative genome analysis of extended spectrum β-lactamase (ESBL)-producing organisms (EPOs) from hospital sewage and clinical samples. Residual antibiotics in the sewage tank were also measured.<br><br>Methods: Metagenomic analysis was performed on the hospital sewage samples, followed by whole genome sequencing of EPOs.<br><br>Results: The bacterial composition of new sewage tanks was comparable with that of old tanks within 1 month after relocation and was instantly affected by excrement. The bacterial composition of sewage tanks in the old and new buildings, containing rooms where seriously ill patients were treated, was similar. Selection on CHROMagar ESBL allowed detection of EPOs harboring bla CTX-M and carbapenemase genes in all sewage tanks. One of the sewage Escherichia coli strain comprising ST393 harboring bla CTX-M-27 corresponded to the clinical isolates based on core genome analysis. Moreover, the levels of levofloxacin and clarithromycin in the hospital sewage were 0.0325 and 0.0135 µg/mL, respectively.<br><br>Conclusion: Hospital sewage was contaminated with many ARB species, ARGs and residual antibiotics, which can cause a burden on WWTP sewage treatment. The bacterial flora in the sewage tank was rapidly affected, especially by the ward with seriously ill patients. AMR monitoring of hospital sewage may help detect carriers prior to nosocomial ARB-associated outbreaks and control the outbreaks.}, }
@article {pmid34983966, year = {2022}, author = {Harvey, E and Holmes, EC}, title = {Diversity and evolution of the animal virome.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {34983966}, issn = {1740-1534}, abstract = {The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their diversity than that of any other biological entity. Most documented animal viruses have been sampled from just two phyla - the Chordata and the Arthropoda - with a strong bias towards viruses that infect humans or animals of economic and social importance, often in association with strong disease phenotypes. Fortunately, the recent development of unbiased metagenomic next-generation sequencing is providing a richer view of the animal virome and shedding new light on virus evolution. In this Review, we explore our changing understanding of the diversity, composition and evolution of the animal virome. We outline the factors that determine the phylogenetic diversity and genomic structure of animal viruses on evolutionary timescales and show how this impacts assessment of the risk of disease emergence in the short term. We also describe the ongoing challenges in metagenomic analysis and outline key themes for future research. A central question is how major events in the evolutionary history of animals, such as the origin of the vertebrates and periodic mass extinction events, have shaped the diversity and evolution of the viruses they carry.}, }
@article {pmid34329532, year = {2022}, author = {O'Connell, KA and Mulder, KP and Wynn, A and de Queiroz, K and Bell, RC}, title = {Genomic library preparation and hybridization capture of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based single nucleotide polymorphism data sets.}, journal = {Molecular ecology resources}, volume = {22}, number = {2}, pages = {487-502}, doi = {10.1111/1755-0998.13481}, pmid = {34329532}, issn = {1755-0998}, mesh = {Formaldehyde ; Genomic Library ; High-Throughput Nucleotide Sequencing ; Isoenzymes ; *Metagenomics ; Phylogeny ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture-based samples clustered together, but RADseq samples did not cluster with corresponding capture-based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.}, }
@article {pmid34982994, year = {2022}, author = {Su, H and Hu, X and Xu, W and Xu, Y and Wen, G and Cao, Y}, title = {Diversity, abundances and distribution of antibiotic resistance genes and virulence factors in the South China Sea revealed by metagenomic sequencing.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152803}, doi = {10.1016/j.scitotenv.2021.152803}, pmid = {34982994}, issn = {1879-1026}, abstract = {Antibiotic resistance genes (ARGs) and virulence factors (VFs) pose considerable health risks to humans. The occurrence and abundance of several typical ARGs in the sea have been widely investigated. However, the full profiles and abundances of the antibiotic resistome and VFs in the South China Sea remain unexplored. Therefore, iIn this study, we investigated the full profiles of the ARGs and VFs, as well as their abundances and distribution, in the South China Sea using metagenomic approaches. In total, 140 ARG subtypes and 155 VFs were detected. The most abundant ARG was multidrug resistance gene, followed by bacitracin resistance gene. Flagella was the most abundant VF. Pearson correlation analysis revealed a strong and positive correlation between the abundances of ARGs and VFs. Redundancy analysis and co-occurrence network analysis showed that the predominant VFs were positively correlated with the predominant ARGs in the South China Sea. Nonmetric multidimensional scaling and Procrustes analyses demonstrated that the sampling sites were clustered into three compartments according to the geographical location, i.e., offshore, open sea, and reef zones. The abundances of ARGs and VFs in the offshore zone were much higher than those in the open sea and reef zones (p < 0.05). Several physico-chemical factors most closely associated with anthropogenic activities, i.e., nitrate, lead, copper, and zinc, were positively correlated with the predominant ARGs and VFs in the South China Sea. Our results suggest that the ocean is a large reservoir of diverse and abundant ARGs and VFs, which may threaten human health and seafood safety. These findings improve the understanding of the relationship between ARG dissemination and intensive anthropogenic activities and can aid in improving ocean management and seafood product safety.}, }
@article {pmid34982977, year = {2021}, author = {Ping, Q and Yan, T and Wang, L and Li, Y and Lin, Y}, title = {Insight into using a novel ultraviolet/peracetic acid combination disinfection process to simultaneously remove antibiotics and antibiotic resistance genes in wastewater: Mechanism and comparison with conventional processes.}, journal = {Water research}, volume = {210}, number = {}, pages = {118019}, doi = {10.1016/j.watres.2021.118019}, pmid = {34982977}, issn = {1879-2448}, abstract = {In this study, the simultaneous removal mechanism of antibiotics and antibiotic resistance genes (ARGs) was investigated using the novel ultraviolet/peracetic acid (UV/PAA) combination disinfection process and conventional disinfection processes were also applied for comparison. The results showed that UV/PAA disinfection with a high UV dosage (UV/PAA-H) was most effective for the removal of tetracyclines, quinolones, macrolides and β-lactams; their average removal efficiencies ranged from 25.7% to 100%, while NaClO disinfection was effective for the removal of sulfonamides (∼81.6%). The majority of ARGs were well removed after the UV/PAA-H disinfection, while specific genes including tetB, tetC, ermA and blaTEM significantly increased after NaClO disinfection. In addition, β-lactam resistance genes (-35.9%) and macrolides resistance genes (-12.0%) remarkably augmented after UV/NaClO disinfection. The highly reactive oxidation species generated from UV/PAA process including hydroxyl radicals (•OH) and carbon-centered organic radicals (R-C•), were responsible for the elimination of antibiotics and ARGs. Correlation analysis showed that tetracycline, sulfonamide and macrolide antibiotics removal showed a positive correlation with the corresponding ARGs, and a low dose of antibiotic residues played an important role in the distribution of ARGs. Metagenomic sequencing analysis showed that UV/PAA disinfection could not only greatly decrease the abundance of resistant bacteria but also downregulate the expression of key functional genes involved in ARGs propagation and inhibit the signal transduction of the host bacteria, underlying that its removal mechanism was quite different from that of NaClO-based disinfection processes. Our study provides valuable information for understanding the simultaneous removal mechanism of antibiotics and ARGs in wastewater during the disinfection processes, especially for the novel UV/PAA combination process.}, }
@article {pmid34982232, year = {2022}, author = {Aravindraja, C and Viszwapriya, D and Valliammai, A and Pandian, SK}, title = {Community-Based 16S rDNA Fingerprinting Analysis of Geographically Distinct Marine Sediments of Unexplored Coastal Regions of Palk Bay and Gulf of Mannar.}, journal = {Current microbiology}, volume = {79}, number = {2}, pages = {60}, pmid = {34982232}, issn = {1432-0991}, abstract = {The present study aims to carefully delineate the bacterial community composition in marine sediments from different geographical coastal regions of Palk Bay and Gulf of Mannar that are known for human recreational activities. Bacterial richness in different marine sediments was assessed using 16S rRNA gene-based Denaturing Gradient Gel Electrophoresis (DGGE) which is a widely deployed fingerprinting technique. The DGGE profiles revealed that the bacterial community profiles of sediment from different coastal regions were complex and dynamic. The most dominant phylum present in the marine sediment samples were Proteobacteria followed by Cyanobacteria, Bacteriodetes, Firmicutes, Acidobacteria, and Actinobacteria. Cosmopolitan presence of Thioalkalivibrio sp. was observed in all the marine sediments. Sequencing of the abundant band reveals the presence of Vibrio spp. in all the marine sediments. Comparative illumina data analysis revealed the presence of 51 different Vibrio species in which Vibrio alginolyticus holds the highest abundance (67.2%) followed by V. harveyi (13.5%). This is the one of the very few reports that compared the complex microbial community composition of the marine sediments of different geographical regions of unexplored coastal region. Further in-depth analysis needs to be taken to understand the presence of complex microbial compositions and their functions through high-throughput whole metagenome sequencing and metaproteomic approaches.}, }
@article {pmid34981990, year = {2022}, author = {Peta, V and Tantely, LM and Potts, R and Girod, R and Pietri, JE}, title = {A Francisella tularensis-Like Bacterium in Tropical Bed Bugs from Madagascar.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {}, number = {}, pages = {}, doi = {10.1089/vbz.2021.0079}, pmid = {34981990}, issn = {1557-7759}, abstract = {The genus Francisella includes several highly virulent human pathogens and some tick endosymbionts. Francisella infections are acquired by humans through contact with vertebrate animal reservoirs or contaminated water or dust. The species Francisella tularensis can also be transmitted by arthropods including ticks, mosquitoes, and flies. For the first time, we describe the molecular detection of an F. tularensis-like bacterium in bed bugs from samples collected in rural Madagascar. This finding suggests a potential involvement of bed bugs in the ecology of Francisella. The role of bed bugs as possible hosts, reservoirs, or vectors of Francisella spp. should be further investigated.}, }
@article {pmid34981906, year = {2022}, author = {Dias, D and Cruz, A and Fonseca, C and Mendo, S and Caetano, TS}, title = {Antibiotic resistance and potential bacterial pathogens identified in red deer's faecal DNA.}, journal = {Transboundary and emerging diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/tbed.14448}, pmid = {34981906}, issn = {1865-1682}, abstract = {In the last decades, the wildlife-human interface has been increasing due to several anthropogenic factors. Therefore, it is crucial to be aware of the impact of these new dynamics on the health of wild animals and its associated zoonotic disease risks. This study aimed to characterise the faecal microbiota of two populations of red deer (Cervus elaphus) by metabarcoding, with a particular focus on potential human and veterinary pathogens, and to perform an assessment of antibiotic resistance genes (ARGs) ocorrence. The faecal microbiota of red deer was assessed by metabarcoding using the 16S rRNA marker, and OTUs of the genera Treponema, Yersinia, Clostridium, Mycobacterium and Rickettsia were identified. Two of them affiliated with species more commonly regarded as pathogens (Clostridium piliforme and Yersinia enterocolitica). The quantification of ARGs was performed by quantitative real-time PCR, using a metagenomic approach, and the most abundant genes were found to be blaTEM , sul1, tetracycline resistance genes (tetW, tetO and tetQ) and ermF. From these, tetO and tetW are rank II ARGs, which were recently considered future threats for human health. Our results suggest the need for screening programs for the occurrence of pathogens and ARGs in wildlife and particularly in game species. This article is protected by copyright. All rights reserved.}, }
@article {pmid34981436, year = {2022}, author = {Gao, Y and Qu, M and Song, C and Yin, L and Zhang, M}, title = {Cerebral vasculitis caused by Talaromyces marneffei and Aspergillus niger in a HIV-positive patient: a case report and literature review.}, journal = {Journal of neurovirology}, volume = {}, number = {}, pages = {}, pmid = {34981436}, issn = {1538-2443}, abstract = {Cerebral vasculitis is a long-standing but flourishing and fadeless research topic. Infections are a frequent cause of cerebral vasculitis, vital to diagnose due to involvement of specific anti-infection treatments. A 65-year-old man visited the hospital for his neurological symptoms without obvious inducements. After admission, radiological examination and comprehensive conventional microbiological tests (CMTs) revealed suspected intracranial infectious vasculitis. Metagenomic next-generation sequencing (mNGS) and reverse transcription-polymerase chain reaction further confirmed that his cerebral vasculitis was caused by Talaromyces marneffei (T. marneffei) and Aspergillus niger (A. niger) co-infection. The patient's final diagnosis changed from initial herpetic encephalitis, due to the past history of cephalosome and facial herpes and non-significant antiviral therapeutic effects, to fungal cerebral vasculitis. The patient was discharged after use of targeted antifungal therapies on day 18 of his admission, and his associated symptoms disappeared completely at follow-up 3 weeks later. We first illustrated the presence of uncommon cerebral vasculitis caused by T. marneffei and A. niger in a human immunodeficiency virus-positive patient. In clinically suspected patients with infectious cerebral vasculitis, mNGS should be performed to detect potential pathogens if CMTs may not provide useful pathogenic clues, highlighting the importance of mNGS in the diagnosis and treatment of infectious diseases.}, }
@article {pmid34980918, year = {2022}, author = {Liu, X and Tong, X and Zou, Y and Lin, X and Zhao, H and Tian, L and Jie, Z and Wang, Q and Zhang, Z and Lu, H and Xiao, L and Qiu, X and Zi, J and Wang, R and Xu, X and Yang, H and Wang, J and Zong, Y and Liu, W and Hou, Y and Zhu, S and Jia, H and Zhang, T}, title = {Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {34980918}, issn = {1546-1718}, abstract = {The gut microbiome has been implicated in a variety of physiological states, but controversy over causality remains unresolved. Here, we performed bidirectional Mendelian randomization analyses on 3,432 Chinese individuals with whole-genome, whole-metagenome, anthropometric and blood metabolic trait data. We identified 58 causal relationships between the gut microbiome and blood metabolites, and replicated 43 of them. Increased relative abundances of fecal Oscillibacter and Alistipes were causally linked to decreased triglyceride concentration. Conversely, blood metabolites such as glutamic acid appeared to decrease fecal Oxalobacter, and members of Proteobacteria were influenced by metabolites such as 5-methyltetrahydrofolic acid, alanine, glutamate and selenium. Two-sample Mendelian randomization with data from Biobank Japan partly corroborated results with triglyceride and with uric acid, and also provided causal support for published fecal bacterial markers for cancer and cardiovascular diseases. This study illustrates the value of human genetic information to help prioritize gut microbial features for mechanistic and clinical studies.}, }
@article {pmid34980915, year = {2022}, author = {Teufel, F and Almagro Armenteros, JJ and Johansen, AR and Gíslason, MH and Pihl, SI and Tsirigos, KD and Winther, O and Brunak, S and von Heijne, G and Nielsen, H}, title = {SignalP 6.0 predicts all five types of signal peptides using protein language models.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {34980915}, issn = {1546-1696}, support = {2017.0323//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 621-2014-3713//Vetenskapsrådet (Swedish Research Council)/ ; }, abstract = {Signal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from sequence data, but existing algorithms are unable to detect all known types of SPs. We introduce SignalP 6.0, a machine learning model that detects all five SP types and is applicable to metagenomic data.}, }
@article {pmid34980911, year = {2022}, author = {Bickhart, DM and Kolmogorov, M and Tseng, E and Portik, DM and Korobeynikov, A and Tolstoganov, I and Uritskiy, G and Liachko, I and Sullivan, ST and Shin, SB and Zorea, A and Andreu, VP and Panke-Buisse, K and Medema, MH and Mizrahi, I and Pevzner, PA and Smith, TPL}, title = {Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {34980911}, issn = {1546-1696}, support = {5090-31000-026-00-D//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 3040-31000-100-00D//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 5090-31000-026-00-D//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 3040-31000-100-00D//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 1715911//National Science Foundation (NSF)/ ; 1715911//National Science Foundation (NSF)/ ; R44AI150008//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R44AI162570//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R44AI150008//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R44AI162570//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R44AI150008//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R44AI162570//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 1947/19//Israel Science Foundation (ISF)/ ; }, abstract = {Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with Hi-C binning can address this challenge even for complex microbial communities. Using existing methods, we sequenced the sheep fecal metagenome and identified 428 MAGs with more than 90% completeness, including 44 MAGs in single circular contigs. To resolve closely related strains (lineages), we developed MAGPhase, which separates lineages of related organisms by discriminating variant haplotypes across hundreds of kilobases of genomic sequence. MAGPhase identified 220 lineage-resolved MAGs in our dataset. The ability to resolve closely related microbes in complex microbial communities improves the identification of biosynthetic gene clusters and the precision of assigning mobile genetic elements to host genomes. We identified 1,400 complete and 350 partial biosynthetic gene clusters, most of which are novel, as well as 424 (298) potential host-viral (host-plasmid) associations using Hi-C data.}, }
@article {pmid34980421, year = {2022}, author = {Tamang, JP and Das, S and Kharnaior, P and Pariyar, P and Thapa, N and Jo, SW and Yim, EJ and Shin, DH}, title = {Shotgun metagenomics of Cheonggukjang, a fermented soybean food of Korea: Community structure, predictive functionalities and amino acids profile.}, journal = {Food research international (Ottawa, Ont.)}, volume = {151}, number = {}, pages = {110904}, doi = {10.1016/j.foodres.2021.110904}, pmid = {34980421}, issn = {1873-7145}, abstract = {Cheonggukjang is a naturally fermented soybean food of Korea. The present study was aimed to reveal the whole microbial community structure of naturally fermented cheonggukjang along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. Metataxonomic profile of cheonggukjang samples showed different domains viz. bacteria (95.83%), virus (2.26%), unclassified (1.84%), eukaryotes (0.05%) and archaea (0.005%). Overall, 44 phyla, 286 families, 722 genera and 1437 species were identified. Firmicutes was the most abundant phylum (98.04%) followed by Proteobacteria (1.49%), Deinococcus-Thermus (0.14%). Bacillus thermoamylovorans was the most abundant species in cheonggukjang followed by Bacillus licheniformis, Bacillus glycinifermentans, Bacillus subtilis, Bacillus paralicheniformis, Bacillus amyloliquifaciens, Brevibacillus borstelensis, Brevibacillus sonorensis Brevibacillus, Acinetobacter, Carnobacterium, Paenibacillus, Cronobacter Enterococcus, Enterobacter, Terriglobus, Psychrobacter and Virgibacillus. A colossal diversity of the genus Bacillus was detected with 150 species. Functional analysis of cheonggukjang metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including, various essential amino acids, conjugated amino acids, different vitamins, flavonoids, and enzymes. Amino acid profiles obtained from KEGG annotation in cheonggukjang were validated with experimental result of amino acid profiles.}, }
@article {pmid34980387, year = {2022}, author = {Zeng, X and Wang, Y and Jia, H and Wang, Z and Gao, Z and Luo, Y and Sheng, Q and Yuan, Y and Yue, T}, title = {Metagenomic analysis of microflora structure and functional capacity in probiotic Tibetan kefir grains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {151}, number = {}, pages = {110849}, doi = {10.1016/j.foodres.2021.110849}, pmid = {34980387}, issn = {1873-7145}, abstract = {Tibetan kefir grains (TKGs) are distinctive and complex mixtures with protein-lipid-polysaccharide matrices and multiple microorganism species. The objective of this study was to evaluate the microflora composition, probiotic species and functional genes within TKGs. Metagenomic analysis was used to evaluate communities of three TKGs, revealing the presence of 715 species, with Lactobacillus kefiranofaciens as the most dominant species. The relative abundances of acetic acid bacteria and yeast significantly differed among the three TKGs (acetic acid bacteria: p < 0.01; yeast: p < 0.05), and the dominant yeast species also varied across three TKGs. Lactobacillus helveticus was the most abundant listed probiotic species, and its abundance did not significantly differ across three TKGs. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that ko01501 was the most abundant pathway that related to human disease. There are 16 different KOs (KEGG Orthology) in the ko01501 pathway were annotated in TKGs, which helps to resist β-lactam. This study provided a new insight into the microbial community structures and the presence of probiotic species within TKGs and provides a foundation for further targeted studies.}, }
@article {pmid34980289, year = {2022}, author = {Yang, Y and Sun, J and Chen, C and Zhou, Y and Van Dover, CL and Wang, C and Qiu, JW and Qian, PY}, title = {Metagenomic and metatranscriptomic analyses reveal minor-yet-crucial roles of gut microbiome in deep-sea hydrothermal vent snail.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {3}, pmid = {34980289}, issn = {2524-4671}, support = {DY135-E2-1-03//China Ocean Mineral Resources Research and Development Association/ ; GML2019ZD0409//the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 2019B030302004-04//the Major Basic and Applied Basic Research Projects of Guangdong Province/ ; SMSEGL20SC01//the Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 91951201//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Marine animals often exhibit complex symbiotic relationship with gut microbes to attain better use of the available resources. Many animals endemic to deep-sea chemosynthetic ecosystems host chemoautotrophic bacteria endocellularly, and they are thought to rely entirely on these symbionts for energy and nutrition. Numerous investigations have been conducted on the interdependence between these animal hosts and their chemoautotrophic symbionts. The provannid snail Alviniconcha marisindica from the Indian Ocean hydrothermal vent fields hosts a Campylobacterial endosymbiont in its gill. Unlike many other chemosymbiotic animals, the gut of A. marisindica is reduced but remains functional; yet the contribution of gut microbiomes and their interactions with the host remain poorly characterised.<br><br>RESULTS: Metagenomic and metatranscriptomic analyses showed that the gut microbiome of A. marisindica plays key nutritional and metabolic roles. The composition and relative abundance of gut microbiota of A. marisindica were different from those of snails that do not depend on endosymbiosis. The relative abundance of microbial taxa was similar amongst three individuals of A. marisindica with significant inter-taxa correlations. These correlations suggest the potential for interactions between taxa that may influence community assembly and stability. Functional profiles of the gut microbiome revealed thousands of additional genes that assist in the use of vent-supplied inorganic compounds (autotrophic energy source), digest host-ingested organics (carbon source), and recycle the metabolic waste of the host. In addition, members of five taxonomic classes have the potential to form slime capsules to protect themselves from the host immune system, thereby contributing to homeostasis. Gut microbial ecology and its interplay with the host thus contribute to the nutritional and metabolic demands of A. marisindica.<br><br>CONCLUSIONS: The findings advance the understanding of how deep-sea chemosymbiotic animals use available resources through contributions from gut microbiota. Gut microbiota may be critical in the survival of invertebrate hosts with autotrophic endosymbionts in extreme environments.}, }
@article {pmid34979467, year = {2021}, author = {Lindner, BG and Suttner, B and Zhu, KJ and Conrad, RE and Rodriguez-R, LM and Hatt, JK and Brown, J and Konstantinidis, KT}, title = {Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms.}, journal = {Water research}, volume = {210}, number = {}, pages = {117993}, doi = {10.1016/j.watres.2021.117993}, pmid = {34979467}, issn = {1879-2448}, abstract = {Little is known about the genomic diversity of the microbial communities associated with raw municipal wastewater (sewage), including whether microbial populations specific to sewage exist and how such populations could be used to improve source attribution and apportioning in contaminated waters. Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) to perturb laboratory freshwater mesocosms, simulating sewage contamination events, and followed these mesocosms with shotgun metagenomics over a 7-day observational period. We describe 15 abundant non-redundant bacterial metagenome-assembled genomes (MAGs) ubiquitous within all sewage inocula yet absent from the unperturbed freshwater control at our analytical limit of detection. Tracking the dynamics of the populations represented by these MAGs revealed varied decay kinetics, depending on (inferred) phenotypes, e.g., anaerobes decayed faster than aerobes under the well-aerated incubation conditions. Notably, a portion of these populations showed decay patterns similar to those of common markers, Enterococcus and HF183. Despite the apparent decay of these populations, the abundance of β-lactamase encoding genes remained high throughout incubation relative to the control. Lastly, we constructed genomic libraries representing several different fecal sources and outline a bioinformatic approach which leverages these libraries for identifying and apportioning contamination signal among multiple probable sources using shotgun metagenomic data.}, }
@article {pmid34979323, year = {2021}, author = {Mao, G and Wu, Y and Zhang, Y and Wang, X and Zhu, Y and Liu, B and Wang, Y and Li, J}, title = {DRBin: Metagenomic binning based on deep representation learning.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2021.12.005}, pmid = {34979323}, issn = {1673-8527}, }
@article {pmid34979278, year = {2021}, author = {Huang, Y and Yang, H and Li, K and Meng, Q and Wang, S and Wang, Y and Zhu, P and Niu, Q and Yan, H and Li, X and Li, Q}, title = {Red mud conserved compost nitrogen by enhancing nitrogen fixation and inhibiting denitrification revealed via metagenomic analysis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {126654}, doi = {10.1016/j.biortech.2021.126654}, pmid = {34979278}, issn = {1873-2976}, abstract = {The objective of this study was to investigate the effects of adding red mud (RM) on denitrification and nitrogen fixation in composting. The results revealed that the retentions of NH4+-N and NO3--N in experimental group (T) with RM were 16.20% and 7.27% higher than that in control group (CK) at the mature stage, respectively. The composition and structure of RM can effectively inhibit denitrification and enhance nitrogen fixation. Moreover, metagenomic analysis revealed that Actinobacteria and Proteobacteria were the main microorganisms in denitrification process, while Firmicutes were the main microorganisms in nitrogen fixation process. In T, denitrifying genes nirK and nosZ were 11% and 18% lower than those in CK, respectively, while nitrogen-fixing genes nifK and nifD were 18% and 34% higher than those in control group, respectively. Therefore, adding RM could reduce nitrogen loss and improve the quality of compost via enhancing nitrogen fixation and inhibiting denitrification process.}, }
@article {pmid34979227, year = {2021}, author = {Wang, W and Zhao, Z and Yan, H and Zhang, H and Li, QX and Liu, X}, title = {Carboxylesterases from bacterial enrichment culture degrade strobilurin fungicides.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152751}, doi = {10.1016/j.scitotenv.2021.152751}, pmid = {34979227}, issn = {1879-1026}, abstract = {Strobilurin fungicides are a class of persistent fungicides frequently detected in the environment. Microbes can effectively degrade strobilurins, but the mechanisms are complex and diverse. Compared with isolated strains, bacterial consortia are more robust in terms of the degradation of multiple pollutants. The enrichment culture XS19 is a group of bacterial strains enriched from soil and degrades six strobilurins at 50 mg/L within 8 d, including azoxystrobin, picoxystrobin, trifloxystrobin, kresoxim-methyl, pyraclostrobin and enestroburin. LC-Q-TOF-MS analysis confirmed that XS19 can demethylate these strobilurins via hydrolysis of the methyl ester group. Analysis of the bacterial communities suggested that Pseudomonas (69.8%), Sphingobacterium (21.2%), Delftia (6.3%), and Achromobacter (1.6%) spp. were highly associated with the removal of strobilurins in the system. Metagenomics-based comprehensive analysis of XS19 suggested that carboxylesterases in Pseudomonas and Sphingobacterium play a central role in the catabolism of strobilurins. Moreover, the carboxylesterase inhibitor bis-p-nitrophenyl phosphate inhibited the degradation activity of strobilurins in XS19. This work proved that XS19 or carboxylesterases can effectively hydrolyze strobilurins, providing a reliable bioremediation paradigm.}, }
@article {pmid34978617, year = {2022}, author = {Mathan Kumar, R and Jani, K and Parvathi, JR and Thomas, BM and Raja, SSS and Pandey, A and Sharma, A}, title = {Bacterial diversity of geochemically distinct hot springs located in Maharashtra, India.}, journal = {Archives of microbiology}, volume = {204}, number = {1}, pages = {110}, pmid = {34978617}, issn = {1432-072X}, support = {BT/Coord.II/01/03/2016//Department of Biotechnology , Ministry of Science and Technology/ ; }, abstract = {Bacterial diversity of four thermally different hot springs of Ratnagiri district, Maharashtra, India, was investigated using culture-dependent and culture-independent approaches. A total of 144 bacterial cultures were isolated and identified using MALDI-TOF MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) and 16S rRNA gene sequencing. Culture-independent analysis by Ion Torrent sequencing targeting the V3 region of the 16S rRNA gene revealed the predominance of Firmicutes across all the hot springs, followed by Chloroflexi, Bacteroidetes, Cyanobacteria, Proteobacteria, Armatimonadetes, Actinobacteria, Nitrospirae, Acidobacteria, and Deinococcus-Thermus, with subtle differences in their abundance. At the lower taxonomic rank of genus, we noted the prevalence of Acinetobacter followed by Clostridium, Planomicrobium, Bacillus, Streptomyces, and Leptolyngbya. Metagenomics imputation using in silico approach revealed divergence in the metabolic capabilities of bacterial communities along the thermal gradient of host springs, with site TS (63 °C) featuring the abundant functional gene families.}, }
@article {pmid34978609, year = {2022}, author = {Bonomo, MG and Calabrone, L and Scrano, L and Bufo, SA and Di Tomaso, K and Buongarzone, E and Salzano, G}, title = {Metagenomic monitoring of soil bacterial community after the construction of a crude oil flowline.}, journal = {Environmental monitoring and assessment}, volume = {194}, number = {2}, pages = {48}, pmid = {34978609}, issn = {1573-2959}, abstract = {This study aimed to assess the metagenomic changes of soil bacterial community after constructing a crude oil flowline in Basilicata region, Italy. Soils identified a total of 56 taxa at the phylum level and 485 at the family level, with a different taxa distribution, especially in samples collected on 2014. Since microbiological diversity occurred in the soils collected after 2013 (the reference year), we performed a differential abundance analysis using DESeq2 by GAIA pipeline. In the forest area, 14 phyla and 126 families were differentially abundant (- 6.06 < logFC > 7.88) in 2014 compared to 2013. Nine families were differentially abundant in 2015, with logFC between - 3.16 and 4.66, while 20 families were significantly more abundant and 16 less abundant in 2016, with logFC between - 6.48 and 6.45. In the cultivated area, 33 phyla and 260 families showed differential abundance in 2014. In the next year (2015), 14 phyla were significantly more abundant and 19 less abundant, while 29 families were substantially more abundant and 139 less abundant, with fold changes ranging between - 5.67 and 4.01. In 2016, 33 phyla showed a significantly different abundance, as 14 were more abundant and 19 decreased, and 81 families showed a significantly increased amount with logFC between - 5.31 and 5.38. These results hypothesise that the analysed site is an altered soil where the development of particular bacterial groups attends to bioremediation processes, naturally occurring to restore optimal conditions.}, }
@article {pmid34978087, year = {2022}, author = {Ning, S and Dai, Z and Zhao, C and Feng, Z and Jin, K and Yang, S and Shen, Q and Wang, X and Sun, R and Zhang, W}, title = {Novel putative pathogenic viruses identified in pangolins by mining metagenomic data.}, journal = {Journal of medical virology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jmv.27564}, pmid = {34978087}, issn = {1096-9071}, abstract = {The pangolin is the only scaly mammal in the world, and also an important reservoir of pathogenic viruses. Habitat loss and poaching have been shrinking the survival range of pangolins. More information on pangolin virus populations is needed to better understand and assess potential disease risks. In this study, viral metagenomics were uesd to re-investigate the virome in pangolin lung tissue. Complete genome sequences of two novel anelloviruses were acquired and clustered with the referenced feline strains belong to genus Tettorquevirus and genus Etatorquevirus, respectively. Two genomes belonging to the genus Gemykibivirus, and species Bat associated cyclovirus 9 were detected, respectively. One genome with a large contig belonging to the genus Senecavirus were also characterized, according to phylogenetic analysis, which can be presumed to be a novel species. In addition, a full genome of ERV was assembled from lungs of Chinese pangolin, and this virus may have the possibility of cross-species transmission during the evolution. This virological investigation has increased our understanding of the virome carried by pangolins and provided a reference baseline for possible zoonotic infectious diseases in the future. This article is protected by copyright. All rights reserved.}, }
@article {pmid34977133, year = {2021}, author = {Liu, Y and Gao, P and Wu, Y and Wang, X and Lu, X and Liu, C and Li, N and Sun, J and Xiao, J and Jesus, SG}, title = {The Formation of Antibiotic Resistance Genes in Bacterial Communities During Garlic Powder Processing.}, journal = {Frontiers in nutrition}, volume = {8}, number = {}, pages = {800932}, doi = {10.3389/fnut.2021.800932}, pmid = {34977133}, issn = {2296-861X}, abstract = {Chinese garlic powder (GP) is exported to all countries in the world, but the excess of microorganisms is a serious problem that affects export. The number of microorganisms has a serious impact on the pricing of GP. It is very important to detect and control the microorganism in GP. The purpose of this study was to investigate the contamination and drug resistance of microorganisms during the processing of GP. We used metagenomics and Illumina sequencing to study the composition and dynamic distribution of antibiotic resistance genes (ARGs), but also the microbial community in three kinds of garlic products from factory processing. The results showed that a total of 126 ARG genes were detected in all the samples, which belonged to 11 ARG species. With the processing of GP, the expression of ARGs showed a trend to increase at first and then to decrease. Network analysis was used to study the co-occurrence patterns among ARG subtypes and bacterial communities and ARGs.}, }
@article {pmid34977080, year = {2021}, author = {Wen, B and Cai, L and Cai, Y and Du, X}, title = {Case Report: Metagenomics Next-Generation Sequencing for Diagnosing Cerebral Infarction and Infection Caused by Hematogenous Disseminated Mucormycosis in a Patient With Acute Lymphoblastic Leukemia.}, journal = {Frontiers in medicine}, volume = {8}, number = {}, pages = {779981}, doi = {10.3389/fmed.2021.779981}, pmid = {34977080}, issn = {2296-858X}, abstract = {Disseminated mucormycosis, a serious complication, is associated with high mortality in patients with acute leukemia after chemotherapy. Blood cultures are always negative because of recurrent empirical antifungal treatments. The identification of pathogens is important for diagnosis and therapy. In this case report, we diagnosed culture-negative disseminated mucormycosis with Rhizomucor miehei infection leading to cerebral infarction in a patient with leukemia using metagenomics next-generation sequencing (mNGS) form peripheral blood, cerebral spinal fluid, and bronchoalveolar lavage fluid. mNGS technology can be applied to precisely diagnose culture-negative disseminated mucormycosis.}, }
@article {pmid34976965, year = {2021}, author = {Xue, R and Chen, Y and Rong, H and Wei, R and Cui, Z and Zhou, J and Dong, W and Jiang, M}, title = {Fusion of Chitin-Binding Domain From Chitinolyticbacter meiyuanensis SYBC-H1 to the Leaf-Branch Compost Cutinase for Enhanced PET Hydrolysis.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {9}, number = {}, pages = {762854}, doi = {10.3389/fbioe.2021.762854}, pmid = {34976965}, issn = {2296-4185}, abstract = {Polyethylene terephthalate (PET) is a mass-produced petroleum-based non-biodegradable plastic that contributes to the global plastic pollution. Recently, biocatalytic degradation has emerged as a viable recycling approach for PET waste, especially with thermophilic polyester hydrolases such as a cutinase (LCC) isolated from a leaf-branch compost metagenome and its variants. To improve the enzymatic PET hydrolysis performance, we fused a chitin-binding domain (ChBD) from Chitinolyticbacter meiyuanensis SYBC-H1 to the C-terminus of the previously reported LCCICCG variant, demonstrating higher adsorption to PET substrates and, as a result, improved degradation performance by up to 19.6% compared to with its precursor enzyme without the binding module. For compare hydrolysis with different binding module, the catalytic activity of LCCICCG-ChBD, LCCICCG-CBM, LCCICCG-PBM and LCCICCG-HFB4 were further investigated with PET substrates of various crystallinity and it showed measurable activity on high crystalline PET with 40% crystallinity. These results indicated that fusing a polymer-binding module to LCCICCG is a promising method stimulating the enzymatic hydrolysis of PET.}, }
@article {pmid34976855, year = {2021}, author = {Song, P and Chen, S and Tan, X and Gao, Y and Fu, J and You, Z and Wang, C and Zhao, Q and Pang, F}, title = {Metagenomic Analysis Identifying a Rare Leishmania Infection in an Adult With AIDS.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {764142}, doi = {10.3389/fcimb.2021.764142}, pmid = {34976855}, issn = {2235-2988}, abstract = {Leishmania belongs to a genus of the protozoan parasites that causes leishmaniasis, and includes cutaneous leishmaniasis (CL) and visceral leishmaniasis (VL). In this case, Leishmania amastigotes were found on cytomorphology examination of the bone marrow specimen, followed by 1,076 Leishmania donovani reads using metagenomic next generation sequencing (mNGS). Since being definitely diagnosed with VL/HIV coinfection, the patient was treated with liposomal amphotericin B as the parasite-resistant therapy and was discharged after clinical cure. But nearly a year later, on the mNGS follow-up, L. donovani was detected in the patient's blood plasma specimen with 941 reads, suggesting that a relapse of leishmaniasis had occurred. These results indicate that leishmaniasis still exists in China and may represent a public health concern. This case could be helpful in the differential diagnosis of leishmaniasis, and for determining disease progression, prevention, and control of vectors and reservoir hosts.}, }
@article {pmid34975825, year = {2021}, author = {Pierangeli, GMF and Domingues, MR and de Jesus, TA and Coelho, LHG and Hanisch, WS and Pompêo, MLM and Saia, FT and Gregoracci, GB and Benassi, RF}, title = {Corrigendum: Higher Abundance of Sediment Methanogens and Methanotrophs Do Not Predict the Atmospheric Methane and Carbon Dioxide Flows in Eutrophic Tropical Freshwater Reservoirs.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {822946}, doi = {10.3389/fmicb.2021.822946}, pmid = {34975825}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2021.647921.].}, }
@article {pmid34975791, year = {2021}, author = {Zhang, L and Chen, F and Zeng, Z and Xu, M and Sun, F and Yang, L and Bi, X and Lin, Y and Gao, Y and Hao, H and Yi, W and Li, M and Xie, Y}, title = {Advances in Metagenomics and Its Application in Environmental Microorganisms.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {766364}, doi = {10.3389/fmicb.2021.766364}, pmid = {34975791}, issn = {1664-302X}, abstract = {Metagenomics is a new approach to study microorganisms obtained from a specific environment by functional gene screening or sequencing analysis. Metagenomics studies focus on microbial diversity, community constitute, genetic and evolutionary relationships, functional activities, and interactions and relationships with the environment. Sequencing technologies have evolved from shotgun sequencing to high-throughput, next-generation sequencing (NGS), and third-generation sequencing (TGS). NGS and TGS have shown the advantage of rapid detection of pathogenic microorganisms. With the help of new algorithms, we can better perform the taxonomic profiling and gene prediction of microbial species. Functional metagenomics is helpful to screen new bioactive substances and new functional genes from microorganisms and microbial metabolites. In this article, basic steps, classification, and applications of metagenomics are reviewed.}, }
@article {pmid34975790, year = {2021}, author = {Liu, C and Li, Z and Ding, J and Zhen, H and Fang, M and Nie, C}, title = {Species-Level Analysis of the Human Gut Microbiome Shows Antibiotic Resistance Genes Associated With Colorectal Cancer.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {765291}, doi = {10.3389/fmicb.2021.765291}, pmid = {34975790}, issn = {1664-302X}, abstract = {Colorectal cancer (CRC) is the second leading cause of cancer deaths and continuously increases new cancer cases globally. Accumulating evidence links risks of CRC to antibiotic use. Long-term use and abuse of antibiotics increase the resistance of the gut microbiota; however, whether CRC is associated with antibiotic resistance in gut microbiota is still unclear. In this study, we performed a de novo assembly to metagenomic sequences in 382 CRC patients and 387 healthy controls to obtain representative species-level genome bins (rSGBs) and plasmids and analyzed the abundance variation of species and antibiotic resistance genes (ARGs). Twenty-five species and 65 ARGs were significantly enriched in the CRC patients, and among these ARGs, 12 were multidrug-resistant genes (MRGs), which mainly included acrB, TolC, marA, H-NS, Escherichia coli acrR mutation, and AcrS. These MRGs could confer resistance to fluoroquinolones, tetracyclines, cephalosporins, and rifamycin antibiotics by antibiotic efflux and inactivation. A classification model was built using the abundance of species and ARGs and achieved areas under the curve of 0.831 and 0.715, respectively. Our investigation has identified the antibiotic resistance types of ARGs and suggested that E. coli is the primary antibiotic resistance reservoir of ARGs in CRC patients, providing valuable evidence for selecting appropriate antibiotics in the CRC treatment.}, }
@article {pmid34975785, year = {2021}, author = {Wu, R and Wang, L and Xie, J and Zhang, Z}, title = {Diversity and Function of Wolf Spider Gut Microbiota Revealed by Shotgun Metagenomics.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {758794}, doi = {10.3389/fmicb.2021.758794}, pmid = {34975785}, issn = {1664-302X}, abstract = {Wolf spiders (Lycosidae) are crucial component of integrated pest management programs and the characteristics of their gut microbiota are known to play important roles in improving fitness and survival of the host. However, there are only few studies of the gut microbiota among closely related species of wolf spider. Whether wolf spiders gut microbiota vary with habitats remains unknown. Here, we used shotgun metagenomic sequencing to compare the gut microbiota of two wolf spider species, Pardosa agraria and P. laura from farmland and woodland ecosystems, respectively. The results show that the gut microbiota of Pardosa spiders is similar in richness and abundance. Approximately 27.3% of the gut microbiota of P. agraria comprises Proteobacteria, and approximately 34.5% of the gut microbiota of P. laura comprises Firmicutes. We assembled microbial genomes and found that the gut microbiota of P. laura are enriched in genes for carbohydrate metabolism. In contrast, those of P. agraria showed a higher proportion of genes encoding acetyltransferase, an enzyme involved in resistance to antibiotics. We reconstructed three high-quality and species-level microbial genomes: Vulcaniibacterium thermophilum, Anoxybacillus flavithermus and an unknown bacterium belonging to the family Simkaniaceae. Our results contribute to an understanding of the diversity and function of gut microbiota in closely related spiders.}, }
@article {pmid34974921, year = {2021}, author = {Fernandez-Cassi, X and Timoneda, N and Gonzales-Gustavson, E and Abril, JF and Bofill-Mas, S and Girones, R}, title = {Corrigendum to "A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water" [Int. J. Food Microbiol. 257 (2017) 80-90 10.1016/j.ijfoodmicro.2017.06.001].}, journal = {International journal of food microbiology}, volume = {}, number = {}, pages = {109507}, doi = {10.1016/j.ijfoodmicro.2021.109507}, pmid = {34974921}, issn = {1879-3460}, }
@article {pmid34974193, year = {2021}, author = {Liu, C and Sun, Z and Shali, S and Mei, Z and Chang, S and Mo, H and Xu, L and Pu, Y and Guan, H and Chen, GC and Qi, Q and Quan, Z and Qi, J and Yao, K and Dai, Y and Zheng, Y and Ge, J}, title = {The gut microbiome and microbial metabolites in acute myocardial infarction.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2021.12.007}, pmid = {34974193}, issn = {1673-8527}, abstract = {Emerging evidence has highlighted the role of the gut microbiome in human health. However, the integrative role of the gut microbiome and microbial metabolites in acute myocardial infarction (AMI) remains unclear. The current study profiled the microbial community through 16S rRNA gene sequencing and shotgun metagenomic sequencing, and measured fecal short-chain fatty acids and circulating choline pathway metabolites among 117 new-onset AMI cases and 78 controls. Significant microbial alternations were observed in AMI patients compared with controls (P = 0.001). The abundances of nine species (e.g., Streptococcus salivarius, Klebsiella pneumoniae) were positively associated, and one species (Roseburia hominis) was inversely associated with AMI status and severity. A gut microbial score at disease onset was associated with the risk of major adverse cardiovascular events in 3.2 years (hazard ratio [95% CI]: 2.01 [1.04-4.24]) in AMI patients. The molar proportions of fecal acetate and butyrate were higher, and the circulating levels of choline and carnitine were lower in AMI patients than in controls. In addition, disease classifiers showed that AMI cases and controls had a more distinct pattern in taxonomical composition than in pathways or metabolites. Our findings suggested that microbial composition and functional potentials were associated with AMI status and severity.}, }
@article {pmid34974183, year = {2021}, author = {Khatoon, M and Patel, SH and Pandit, RJ and Jakhesara, SJ and Rank, DN and Joshi, CG and Kunjadiya, AP}, title = {Rumen and fecal microbial profiles in cattle fed high lignin diets using metagenome analysis.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {102508}, doi = {10.1016/j.anaerobe.2021.102508}, pmid = {34974183}, issn = {1095-8274}, abstract = {Coconut coir (a lignin-rich, organic material) is widely used for its commercial and economic benefits. In this study, crossbred (exotic) and Kankrej (indigenous) breeds of cattle were fed diets containing 7 or 14% coconut coir. Metagenomic analyses (16S rRNA gene amplicon and shotgun sequencing) were used to characterize the microbial community in the rumen and fecal samples along with their functional capabilities. Both amplicon and shotgun analyses revealed the predominance of bacterial phyla, Bacteroidetes, Firmicutes, Actinobacteria and Fibrobacter in ruminal liquid, ruminal solid and fecal samples. 16S rRNA gene amplicon sequencing revealed a total of 18 different bacterial taxa were found to be enriched exclusively in the animals fed with 14% coir. The shotgun analysis revealed abundance of bacterial genera, Fibrobacter, Clostridium, Prevotella, Butyrivibrio, and Ruminococcus in both liquid and solid fractions of ruminal contents, while in the fecal sample, Bacteroides, Alistipes, Plaudibacter, Parabacteroides, Porphyromonas, and Victivallis and archaeal genus, Methanocorpusculum were abundant. The functional analysis based on dbCAN database suggested that among the Glycoside hydrolase family, genes that encode oligosaccharide degrading enzymes, GH3, GH13 (p-value < 0.05), and GH43 were abundant in the feces. In ruminal solid, cellulase encoding the GH5 family was abundant. Also, lignocellulosic binding modules encoded by the CBM family, including cellulose (CBM3) and hemicellulose binding modules (CBM32 and CBM67) were abundant. Thus, the study indicated the enrichment of lignocellulosic enzymes in ruminal contents in response to feeding the coconut coir, which could be mined for potential biofuel production and other biotechnological applications.}, }
@article {pmid34974121, year = {2021}, author = {de Lima, AMDL and de Lima Rosa, G and Müller Guzzo, EF and Padilha, RB and Costa da Silva, R and Silveira, AK and de Lima Morales, D and Conci de Araujo, M and Fonseca Moreira, JC and Barth, AL and Coitinho, AS and Van Der Sand, ST}, title = {Gut microbiota modulation by prednisolone in a rat kindling model of pentylenetetrazol (PTZ)-induced seizure.}, journal = {Microbial pathogenesis}, volume = {163}, number = {}, pages = {105376}, doi = {10.1016/j.micpath.2021.105376}, pmid = {34974121}, issn = {1096-1208}, abstract = {The gut microbiota is a complex community composed by several microorganisms that interact in the maintenance of homeostasis and contribute to physiological processes, including brain function. The relationship of the taxonomic composition of the gut microbiota with neurological diseases such as autism, Parkinson's, Alzheimer's, anxiety, and depression is widely recognized. The immune system is an important intermediary between the gut microbiota and the central nervous system, being one of the communication routes of the gut-brain axis. Although the complexity of the relationship between inflammation and epilepsy has not yet been elucidated, inflammatory processes are similar in many ways to the consequences of dysbiosis and contribute to disease progression. This study aimed to analyze the taxonomic composition of the gut microbiota of rats treated with prednisolone in a kindling model of epilepsy. Male Wistar rats (90 days, n = 24) divided into four experimental groups: sodium chloride solution 0.9 g%, diazepam 2 mg/kg, prednisolone 1 mg/kg, and prednisolone 5 mg/kg administered intraperitoneally (i.p.) for 14 days. The kindling model was induced by pentylenetetrazole (PTZ) 25 mg/kg i.p. on alternate days. The taxonomic profile was established by applying metagenomic DNA sequencing. There was no change in alpha diversity, and the composition of the gut microbiota between prednisolone and diazepam was similar. The significant increase in Verrucomicrobia, Saccharibacteria, and Actinobacteria may be related to the protective activity against seizures and inflammatory processes that cause some cases of epilepsy. Further studies are needed to investigate the functional influence that these species have on epilepsy and the inflammatory processes that trigger it.}, }
@article {pmid34974104, year = {2021}, author = {Zhang, X and Ma, D and Lv, J and Feng, Q and Liang, Z and Chen, H and Feng, J}, title = {Food waste composting based on patented compost bins: Carbon dioxide and nitrous oxide emissions and the denitrifying community analysis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {126643}, doi = {10.1016/j.biortech.2021.126643}, pmid = {34974104}, issn = {1873-2976}, abstract = {Mature compost and rice bran were used as bulking agents to perform Food Waste Rapid Composting (FWRC) in a patented composting bin. The characteristics of CO2 and N2O emission and the denitrifying community were investigated. The release of CO2 and N2O concentrated in the early composting stage and reduced greatly after 28 hours, and the N2O emission peak of the treatment with mature compost was 8.5 times higher than that of rice bran. The high N2O generation resulted from massive denitrifying bacteria and NOx--N in the composting material. The relative abundances of denitrifiers, correspondingly genes of narG and nirK were much higher in the treatment with mature compost, which contributed to the N2O emission. Moreover, the correlation matrices revealed that N2O fluxes correlated well with moisture, pH, temperature, and the abundances of nirK and nosZ genes during FWRC.}, }
@article {pmid34974089, year = {2021}, author = {Di Cesare, A and Sabatino, R and Yang, Y and Brambilla, D and Li, P and Fontaneto, D and Eckert, EM and Corno, G}, title = {Contribution of plasmidome, metal resistome and integrases to the persistence of the antibiotic resistome in aquatic environments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {118774}, doi = {10.1016/j.envpol.2021.118774}, pmid = {34974089}, issn = {1873-6424}, abstract = {Wastewater treatment plants (WWTPs) are among the main hotspots of antibiotic resistance genes (ARGs) in the environment. Previously, we demonstrated that by increasing anthropogenic pollution the antibiotic resistome persisted in the microbial community of rivers and lakes, independently by changes in community composition. In this study we reanalysed the data to test for the relation of metal resistance genes (MRGs), plasmids, and integrons to the persistence of the antibiotic resistome. The experiment consisted in replicated co-cultures of riverine or lacustrine microbial communities and WWTP effluents in different proportions. Samples before (T0) and after a short period of incubation (TF) were collected and community metagenomic data were obtained by shotgun sequencing. The data were processed to annotate MRGs, plasmids, and integrases. The integrases stabilized in the aquatic environment following the degree of contamination with effluent water (in particular in one site), whereas MRGs and plasmids showed stochastic trajectories. These results confirm the potential correlation between integrons and anthropogenic pollution, and the reliability of intI1 as a pollution marker. Only in one site MRGs, plasmids, and ARGs were correlated, highlighting their partial contribution to the persistence of ARGs in surface waters.}, }
@article {pmid34973832, year = {2021}, author = {Sonneville, R and Jaquet, P and Vellieux, G and de Montmollin, E and Visseaux, B}, title = {Intensive care management of patients with viral encephalitis.}, journal = {Revue neurologique}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.neurol.2021.12.002}, pmid = {34973832}, issn = {0035-3787}, abstract = {Viral encephalitis is a severe syndrome that can lead to encephalopathy, seizures, focal deficits, and neurological sequelae and death. It is mainly caused by neurotropic herpes viruses (i.e., HSV and VZV), although other pathogens may be observed in specific geographic regions or conditions. Recent advances in neuroimaging and molecular biology (PCR, metagenomics) allow for faster and more accurate etiological diagnoses, although their benefits need to be confirmed to provide guidelines for their use and interpretation. Despite intravenous acyclovir therapy and supportive care, outcomes remain poor in about two-thirds of herpes encephalitis patients requiring ICU admission. Randomized clinical trials focusing on symptomatic measures (i.e. early ICU admission, fever control, and treatment of seizures/status epilepticus) or adjunctive immunomodulatory therapies (i.e. steroids, intravenous immunoglobulins) to improve neurologic outcomes have not been conducted in the ICU setting. Large prospective multicenter studies combining clinical, electrophysiological, and neuroimaging data are needed to improve current knowledge on care pathways, long-term outcomes, and prognostication.}, }
@article {pmid34973527, year = {2021}, author = {Kamel, HL and Hanora, A and Solyman, SM}, title = {Metataxanomic, bioactivity and microbiome analysis of Red Sea marine sponges from Egypt.}, journal = {Marine genomics}, volume = {61}, number = {}, pages = {100920}, doi = {10.1016/j.margen.2021.100920}, pmid = {34973527}, issn = {1876-7478}, abstract = {Red Sea marine sponges (phylum Porifera) and associated microorganisms harbor a wide range of microorganisms, which are considered an essential source of bioactive products. In this study, we screened both the crude extracts of Red Sea marine sponges and their associated bacterial extract for antimicrobial activity and antiviral activity. Molecular characterization of bioactive producers was performed using16S rRNA sequencing, in addition to metagenomic analysis of three representative sponges utilizing the 16S rRNA gene V3-V4 region sequencing in two different seasons. Twelve samples were collected from five different sponge species by scuba diving, and all the crude extracts of sponges showed antimicrobial activity except Negombata corticata. Moreover, 84 out of 110 bacterial isolates extracts demonstrated antimicrobial activity against at least one tested microorganism. These results revealed the bioactivity and biodiversity of the Red Sea marine invertebrates-associated bacteria. It was found that the bioactive isolates belong to several bacterial groups. The bacterial communities of Negombata magnifica, Negombata corticata, and Siphonochalina siphonella were shown with great diversity and differences in the bacterial percentage, diversity, and unique community composition at different seasons in each sponge species. Unique microenvironment for each sponge species may be linked to the production of specific bioactive product.}, }
@article {pmid34973477, year = {2021}, author = {Kim, Y and Lee, S and Kim, S and Kim, TY and Lee, SH and Chang, JH and Kweon, MN}, title = {LKB1 in intestinal epithelial cells regulates bile acid metabolism by modulating FGF15/19 production.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcmgh.2021.12.017}, pmid = {34973477}, issn = {2352-345X}, abstract = {BACKGROUND &amp; AIM: Liver kinase B1 (LKB1) is a master upstream protein kinase involved in nutrient sensing and glucose and lipid metabolism in many tissues; however, its metabolic role in intestinal epithelial cells (IEC) remains unclear. In this study, we investigated the regulatory role of LKB1 on bile acid (BA) homeostasis.<br><br>METHODS: We generated mice with IEC-specific deletion of LKB1 (LKB1ΔIEC) and analyzed the characteristics of IEC development and BA level. In vitro assays with small interfering RNA, liquid chromatography (LC) / mass spectrometry (MS/MS), metagenomics, and RNA-sequencing were used to elucidate the regulatory mechanisms underlying perturbed BA homeostasis.<br><br>RESULTS: LKB1 deletion resulted in abnormal differentiation of secretory cell lineages. Unexpectedly, BA pool size increased substantially in LKB1ΔIEC mice. A significant reduction of the farnesoid X receptor (FXR) target genes, including fibroblast growth factor 15/19 (FGF15/19), known to inhibit BA synthesis, was found in the small intestine (SI) ileum of LKB1ΔIEC mice. We observed that LKB1 depletion reduced FGF15/19 protein level in human IECs in vitro. Additionally, a lower abundance of bile salt hydrolase-producing bacteria and elevated levels of FXR antagonist (i.e., T-βMCA) were observed in the SI of LKB1ΔIEC mice. Moreover, LKB1ΔIEC mice showed impaired conversion of retinol to retinoic acids in the SI ileum. Subsequently, vitamin A treatment failed to induce FGF15 production. Thus, LKB1ΔIEC mice fed with a high-fat diet showed improved glucose tolerance and increased energy expenditure.<br><br>CONCLUSIONS: LKB1 in IECs manages BA homeostasis by controlling FGF15/19 production.}, }
@article {pmid34973371, year = {2021}, author = {Zou, J and Wang, T and Qiu, T and Chen, Z and Zhou, J and Ma, X and Jin, Z and Xu, Y and Zhang, L}, title = {Clinical characteristics of tuberculous infection following renal transplantation.}, journal = {Transplant immunology}, volume = {}, number = {}, pages = {101523}, doi = {10.1016/j.trim.2021.101523}, pmid = {34973371}, issn = {1878-5492}, abstract = {OBJECTIVE: This study investigated the clinical characteristics of patients with tuberculosis (TB) following renal transplantation (RT) in order to identify markers or signs that can facilitate early diagnosis.<br><br>METHODS: A retrospective analysis was performed on 12 cases of Mycobacterium tuberculosis infection treated at our hospital between 2005 and 2020.<br><br>RESULTS: The incidence of TB after RT at our hospital was 0.9%, and the median postoperative onset time was 22 months. The average age of patients included in our analysis was 44.2 ± 9.4 years; 11 of the 12 patients were male, and most patients had (low) fever as the first or only manifestation. Five patients had respiratory symptoms; 5 had typical computed tomography (CT) presentation; and 2 had a confirmed history of TB. Two sputum smears from 12 patients were positive by acid fast staining, and M. tuberculosis was detected in peripheral blood samples by metagenomic next-generation sequencing (NGS). One patient had a positive result in the purified protein derivative (PPD) test, 7 were positive with the interferon gamma release assay (IGRA), 8/12 patients were confirmed to have TB infection by NGS and 1 was confirmed positive by lung biopsy.<br><br>CONCLUSION: Because of the use of immunosuppressive agents, most patients with TB following RT have atypical clinical symptoms and CT findings, and may have a high probability of a false negative result with the traditional PPD test and a low probability of M. tuberculosis detection, making early diagnosis difficult. Therefore, in RT recipients with prolonged fever of unknown origin and unusual clinical manifestations, especially those who are unresponsive to antibiotic treatment, a diagnosis of TB should be considered. The interferon gamma release assay and NGS are relatively new detection methods with high sensitivity and specificity; these along with regular, repeated testing by various approaches can aid the early diagnosis of TB.}, }
@article {pmid34972143, year = {2021}, author = {Tongununui, P and Kuriya, Y and Murata, M and Sawada, H and Araki, M and Nomura, M and Morioka, K and Ichie, T and Ikejima, K and Adachi, K}, title = {Mangrove crab intestine and habitat sediment microbiomes cooperatively work on carbon and nitrogen cycling.}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0261654}, doi = {10.1371/journal.pone.0261654}, pmid = {34972143}, issn = {1932-6203}, abstract = {Mangrove ecosystems, where litter and organic components are degraded and converted into detrital materials, support rich coastal fisheries resources. Sesarmid (Grapsidae) crabs, which feed on mangrove litter, play a crucial role in material flow in carbon-rich and nitrogen-limited mangrove ecosystems; however, the process of assimilation and conversion into detritus has not been well studied. In this study, we performed microbiome analyses of intestinal bacteria from three species of mangrove crab and five sediment positions in the mud lobster mounds, including the crab burrow wall, to study the interactive roles of crabs and sediment in metabolism. Metagenome analysis revealed species-dependent intestinal profiles, especially in Neosarmatium smithi, while the sediment microbiome was similar in all positions, albeit with some regional dependency. The microbiome profiles of crab intestines and sediments were significantly different in the MDS analysis based on OTU similarity; however, 579 OTUs (about 70% of reads in the crab intestinal microbiome) were identical between the intestinal and sediment bacteria. In the phenotype prediction, cellulose degradation was observed in the crab intestine. Cellulase activity was detected in both crab intestine and sediment. This could be mainly ascribed to Demequinaceae, which was predominantly found in the crab intestines and burrow walls. Nitrogen fixation was also enriched in both the crab intestines and sediments, and was supported by the nitrogenase assay. Similar to earlier reports, sulfur-related families were highly enriched in the sediment, presumably degrading organic compounds as terminal electron acceptors under anaerobic conditions. These results suggest that mangrove crabs and habitat sediment both contribute to carbon and nitrogen cycling in the mangrove ecosystem via these two key reactions.}, }
@article {pmid34971956, year = {2021}, author = {Zeng, H and Hu, W and Liu, G and Xu, H and Wei, Y and Zhang, J and Shi, H}, title = {Microbiome-wide association studies between phyllosphere microbiota and ionome highlight the beneficial symbiosis of Lactococcus lactis in alleviating aluminium in cassava.}, journal = {Plant physiology and biochemistry : PPB}, volume = {171}, number = {}, pages = {66-74}, doi = {10.1016/j.plaphy.2021.12.029}, pmid = {34971956}, issn = {1873-2690}, abstract = {The phyllosphere is one of the most abundant habitats for global microbiota. The ionome is the composition of mineral elements in plants. The correlation between phyllosphere microbiota and the ionome remains elusive in plants, especially in the most important tropical crop cassava. In this study, microbiome-wide association studies (MWASs) of thirty varieties were performed to reveal the association between phyllosphere microbiota and ionomic variations in cassava. Annotation of metagenomic species identified some species that were significantly correlated with ionomic variations in cassava. Among them, Lactococcus lactis abundance was negatively associated with leaf aluminium (Al) levels but positively related to leaf potassium (K) levels. Notably, both the reference and isolated L. lactis showed strong binding capacity to Al. Further bacterial transplantation of isolated L. lactis could significantly decrease endogenous Al levels but increase K levels in cassava, and it can also lead to increased citric acid and lactic acid levels as well as higher transcript levels of K uptake-related genes. Taken together, this study reveals the involvement of phyllosphere microbiota in ionomic variation in cassava, and the correlation between L. lactis abundance and Al and K levels provides novel insights into alleviating Al accumulation and promoting K uptake simultaneously.}, }
@article {pmid34970896, year = {2021}, author = {Peng, X and Zhao, Y and Lin, T and Shu, X and Hou, L and Gao, L and Wang, H and Ge, N and Yue, J}, title = {[Research of relationship between frailty and gut microbiota on middle-aged and the aged patients with diabetes].}, journal = {Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi}, volume = {38}, number = {6}, pages = {1126-1133}, doi = {10.7507/1001-5515.202101083}, pmid = {34970896}, issn = {1001-5515}, mesh = {Aged ; *Diabetes Mellitus ; *Epstein-Barr Virus Infections ; *Frailty ; *Gastrointestinal Microbiome ; Herpesvirus 4, Human ; Humans ; Middle Aged ; }, abstract = {Gut microbiota plays an important role in development of diabetes with frailty. Therefore, it is of great significance to study the structural and functional characteristics of gut microbiota in Chinese with frailty. Totally 30 middle-aged and the aged participants in communities with diabetes were enrolled in this study, and their feces were collected. At the same time, we developed a metagenome analysis to explore the different of the structural and functional characteristics between diabetes with frailty and diabetes without frailty. The results showed the alpha diversity of intestinal microbiota in diabetes with frailty was lower. Collinsella and Butyricimonas were more abundant in diabetes with frailty. The functional characteristics showed that histidine metabolism, Epstein-Barr virus infection, sulfur metabolism, and biosynthesis of type Ⅱ polyketide products were upregulated in diabetes with frailty. Otherwise, butanoate metabolism and phenylalanine metabolism were down-regulated in diabetes with frailty. This research provides theoretical basic for exploring the mechanism of the gut microbiota on the occurrence and development of diabetes with frailty, and provides a basic for prevention and intervention of it.}, }
@article {pmid34970720, year = {2021}, author = {Rettenmaier, LA and Abdel-Wahed, L and Abdelmotilib, H and Conway, KS and Narayanan, N and Groth, CL}, title = {COVID-19-associated necrotizing encephalopathy presenting without active respiratory symptoms: a case report with histopathology.}, journal = {Journal of neurovirology}, volume = {}, number = {}, pages = {}, pmid = {34970720}, issn = {1538-2443}, abstract = {Acute necrotizing encephalopathy (ANE) is a rare complication of coronavirus disease 2019 (COVID-19) secondary to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The condition is typically diagnosed based on characteristic neuroimaging findings in the context of active viral respiratory symptoms. We present a rare case of COVID-19-associated ANE presenting with expressive aphasia and encephalopathy in the absence of active respiratory symptoms. Initial evaluation revealed bilateral thalamic lesions and a mild neutrophilic-predominant pleocytosis on cerebrospinal fluid analysis, the latter of which has not been described in previously published cases. Presence of these atypical features prompted extensive diagnostic evaluation. Metagenomic next-generation sequencing on cerebrospinal fluid did not detect the presence of pathogenic nucleic acids. Thalamic biopsy revealed perivascular neutrophilic inflammation suggestive of small vessel vasculitis with surrounding hemorrhage and necrosis. Ultimately, the diagnosis was made following detection of SARS-CoV-2 serologies and after exclusion of alternative etiologies. The patient was successfully treated with a short course of high-dose methylprednisolone with favorable outcome.}, }
@article {pmid34970712, year = {2021}, author = {Shapiro, JT and Mollerup, S and Jensen, RH and Olofsson, JK and Nguyen, ND and Hansen, TA and Vinner, L and Monadjem, A and McCleery, RA and Hansen, AJ}, title = {Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini.}, journal = {EcoHealth}, volume = {}, number = {}, pages = {}, pmid = {34970712}, issn = {1612-9210}, support = {1R01GM114362/NH/NIH HHS/United States ; ACI-1053575//National Science Foundation/ ; Extreme Science//National Science Foundation/ ; Engineering Discovery Environm//National Science Foundation/ ; GRFP DGE-1315138//National Science Foundation/ ; Graduate Research Opportunities Worldwide//National Science Foundation/ ; TG-ASC160034//National Science Foundation/ ; Student Research Grant//Bat Conservation International/ ; The Genome Denmark platform//Innovationsfonden/ ; grant no. 019-2011-2//Innovationsfonden/ ; }, abstract = {We investigated the prevalence of coronaviruses in 44 bats from four families in northeastern Eswatini using high-throughput sequencing of fecal samples. We found evidence of coronaviruses in 18% of the bats. We recovered full or near-full-length genomes from two bat species: Chaerephon pumilus and Afronycteris nana, as well as additional coronavirus genome fragments from C. pumilus, Epomophorus wahlbergi, Mops condylurus, and Scotophilus dinganii. All bats from which we detected coronaviruses were captured leaving buildings or near human settlements, demonstrating the importance of continued surveillance of coronaviruses in bats to better understand the prevalence, diversity, and potential risks for spillover.}, }
@article {pmid34970508, year = {2021}, author = {Jiang, Q and Liu, X and Yang, Q and Chen, L and Yang, D}, title = {Salivary Microbiome in Adenoid Cystic Carcinoma Detected by 16S rRNA Sequencing and Shotgun Metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {774453}, pmid = {34970508}, issn = {2235-2988}, abstract = {Microorganisms are confirmed to be closely related to the occurrence and development of cancers in human beings. However, there has been no published report detailing relationships between the oral microbiota and salivary adenoid cystic carcinoma (SACC). In this study, unstimulated saliva was collected from 13 SACC patients and 10 healthy controls. The microbial diversities, compositions and functions were comprehensively analyzed after 16S rRNA sequencing and whole-genome shotgun metagenomic sequencing. The alpha diversity showed no significant difference between SACC patients and healthy controls, while beta diversity showed a separation trend. The SACC patients showed higher abundances of Streptococcus and Rothia, while Prevotella and Alloprevotella were more abundant in healthy controls. The prevalent KEGG pathways, carbohydrate-active enzymes, antibiotic resistances and virulence factors as well as the biomarkers in SACC were determined by functional gene analysis. Our study preliminarily investigated the salivary microbiome of SACC patients compared with healthy controls and might be the basis for further studies on novel diagnostic and treatment strategies.}, }
@article {pmid34969995, year = {2021}, author = {Bowers, RM and Nayfach, S and Schulz, F and Jungbluth, SP and Ruhl, IA and Sheremet, A and Lee, J and Goudeau, D and Eloe-Fadrosh, EA and Stepanauskas, R and Malmstrom, RR and Kyrpides, NC and Dunfield, PF and Woyke, T}, title = {Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {34969995}, issn = {1751-7370}, abstract = {With advances in DNA sequencing and miniaturized molecular biology workflows, rapid and affordable sequencing of single-cell genomes has become a reality. Compared to 16S rRNA gene surveys and shotgun metagenomics, large-scale application of single-cell genomics to whole microbial communities provides an integrated snapshot of community composition and function, directly links mobile elements to their hosts, and enables analysis of population heterogeneity of the dominant community members. To that end, we sequenced nearly 500 single-cell genomes from a low diversity hot spring sediment sample from Dewar Creek, British Columbia, and compared this approach to 16S rRNA gene amplicon and shotgun metagenomics applied to the same sample. We found that the broad taxonomic profiles were similar across the three sequencing approaches, though several lineages were missing from the 16S rRNA gene amplicon dataset, likely the result of primer mismatches. At the functional level, we detected a large array of mobile genetic elements present in the single-cell genomes but absent from the corresponding same species metagenome-assembled genomes. Moreover, we performed a single-cell population genomic analysis of the three most abundant community members, revealing differences in population structure based on mutation and recombination profiles. While the average pairwise nucleotide identities were similar across the dominant species-level lineages, we observed differences in the extent of recombination between these dominant populations. Most intriguingly, the creek's Hydrogenobacter sp. population appeared to be so recombinogenic that it more closely resembled a sexual species than a clonally evolving microbe. Together, this work demonstrates that a randomized single-cell approach can be useful for the exploration of previously uncultivated microbes from community composition to population structure.}, }
@article {pmid34969947, year = {2021}, author = {Ghanavi, HR and Twort, VG and Duplouy, A}, title = {Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {24499}, pmid = {34969947}, issn = {2045-2322}, support = {6422141//European Union's Horizon 2020 research and innovation program, Marie Sklodowska-Curie grant/ ; 790531//Marie Sklodowska-Curie Individual fellowship/ ; }, abstract = {Models estimate that up to 80% of all butterfly and moth species host vertically transmitted endosymbiotic microorganisms, which can affect the host fitness, metabolism, reproduction, population dynamics, and genetic diversity, among others. The supporting empirical data are however currently highly biased towards the generally more colourful butterflies, and include less information about moths. Additionally, studies of symbiotic partners of Lepidoptera predominantly focus on the common bacterium Wolbachia pipientis, while infections by other inherited microbial partners have more rarely been investigated. Here, we mine the whole genome sequence data of 47 species of Erebidae moths, with the aims to both inform on the diversity of symbionts potentially associated with this Lepidoptera group, and discuss the potential of metagenomic approaches to inform on host associated microbiome diversity. Based on the result of Kraken2 and MetaPhlAn2 analyses, we found clear evidence of the presence of Wolbachia in four species. Our result also suggests the presence of three other bacterial symbionts (Burkholderia spp., Sodalis spp. and Arsenophonus spp.) in three other moth species. Additionally, we recovered genomic material from bracovirus in about half of our samples. The detection of the latter, usually found in mutualistic association to braconid parasitoid wasps, may inform on host-parasite interactions that take place in the natural habitat of the Erebidae moths, suggesting either contamination with material from species of the host community network, or horizontal transfer of members of the microbiome between interacting species.}, }
@article {pmid34969477, year = {2022}, author = {Guo, M and Jiang, Y and Xie, J and Cao, Q and Zhang, Q and Mabruk, A and Chen, C}, title = {Bamboo charcoal addition enhanced the nitrogen removal of anammox granular sludge with COD: Performance, physicochemical characteristics and microbial community.}, journal = {Journal of environmental sciences (China)}, volume = {115}, number = {}, pages = {55-64}, doi = {10.1016/j.jes.2021.07.010}, pmid = {34969477}, issn = {1001-0742}, mesh = {Anaerobic Ammonia Oxidation ; Anaerobiosis ; Biological Oxygen Demand Analysis ; Bioreactors ; Charcoal ; Denitrification ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; Planctomycetes ; *Sewage ; }, abstract = {The effects of different chemical oxygen demand (COD) concentrations on the anammox granular sludge with Bamboo Charcoal (BC) addition were evaluated in UASB reactor. The results showed that the average total nitrogen (TN) removal efficiency was reduced from 85.9% to 81.4% when COD concentration was increased from 50 to 150 mg/L. However, the TN removal efficiency of BC addition reactors was dramatically 3.1%-6.4% higher than that without BC under different COD concentrations. The average diameter of granular sludge was 0.13 mm higher than that without BC. The settling velocity was increased by elevated COD concentration, while the EPS and VSS/SS were increased with BC addition. The high-throughput Miseq sequencing analyses revealed that the bacterial diversity and richness were decreased under COD addition, and the Planctomycetes related to anammox bacteria were Candidatus Brocadia and Candidatus Kuenenia. The Metagenomic sequencing indicated that the abundance of denitrification related functional genes all increased with elevated COD, while the abundance of anammox related functional genes of decreased. The functional genes related to anammox was hydrazine synthase encoding genes (hzsA, hzsB and hzsB). The average relative abundance of hzs genes in the reactor with BC addition was higher than the control at COD concentrations of 50 mg/L and 150 mg/L. The functional genes of denitrification mediated by BC were higher than those without BC throughout the operation phase. It is interesting to note that BC addition greatly enriched the related functional genes of denitrification and anammox.}, }
@article {pmid34969453, year = {2022}, author = {Wang, F and Luo, J and Fang, S and Huang, W and Zhang, Y and Zhang, L and Cheng, X and Du, W and Fang, F and Cao, J and Wu, Y}, title = {Mechanisms of allicin exposure for the sludge fermentation enhancement: Focusing on the fermentation processes and microbial metabolic traits.}, journal = {Journal of environmental sciences (China)}, volume = {115}, number = {}, pages = {253-264}, doi = {10.1016/j.jes.2021.07.024}, pmid = {34969453}, issn = {1001-0742}, mesh = {Disulfides ; *Fatty Acids, Volatile ; Fermentation ; Hydrogen-Ion Concentration ; Hydrolysis ; *Sewage ; Sulfinic Acids ; }, abstract = {As a frequently used product with antimicrobial activity, consumed allicin might be discharged and concentrated in waste-activated sludge (WAS). However, the influence of allicin (as an exogenous pollutant) on WAS fermentation has not been clearly revealed. This study aimed to disclose the impacts of allicin on volatile fatty acid (VFA) generation during WAS fermentation. The results showed that the appropriate presence of allicin (10 mg/g TSS) significantly enhanced the VFA yield (1894 versus 575 mg COD/L in the control) with increased acetate proportion (24.3%). Further exploration found that allicin promoted WAS solubilization, hydrolysis and acidification simultaneously. Metagenomic analysis revealed that the key genes involved in extracellular hydrolysis metabolism (i.e., CAZymes), membrane transport (i.e., gtsA and ytfT), substrate metabolism (i.e., yhdR and pfkC) and fatty acid synthesis (i.e., accA and accD) were all highly expressed. Allicin also induced the bacteria to produce more signalling molecules and regulate cellular functions, thereby enhancing the microbial adaptive and regulatory capacity to the unfavourable environment. Moreover, the variations in fermentative microbes and their contributions to the upregulation of functional genes (i.e., ytfR, gltL, INV, iolD and pflD) for VFA generation were disclosed. Overall, the simultaneous stimulation of functional microbial abundances and metabolic activities contributed to VFA production in allicin-conditioned reactors.}, }
@article {pmid34824209, year = {2021}, author = {Kandathil, AJ and Cox, AL and Page, K and Mohr, D and Razaghi, R and Ghanem, KG and Tuddenham, SA and Hsieh, YH and Evans, JL and Coller, KE and Timp, W and Celentano, DD and Ray, SC and Thomas, DL}, title = {Plasma virome and the risk of blood-borne infection in persons with substance use disorder.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6909}, pmid = {34824209}, issn = {2041-1723}, support = {U19 AI159822/AI/NIAID NIH HHS/United States ; R01 DA016017/DA/NIDA NIH HHS/United States ; R21 DA053145/DA/NIDA NIH HHS/United States ; }, mesh = {Adult ; Amino Acid Sequence ; Anelloviridae ; *Blood-Borne Infections ; Blood-Borne Pathogens ; Female ; Hepatitis C/epidemiology ; Humans ; Knowledge ; Male ; Metagenomics ; Phylogeny ; *Plasma ; Public Health ; *Substance-Related Disorders ; *Virome ; Young Adult ; }, abstract = {There is an urgent need for innovative methods to reduce transmission of bloodborne pathogens like HIV and HCV among people who inject drugs (PWID). We investigate if PWID who acquire non-pathogenic bloodborne viruses like anelloviruses and pegiviruses might be at greater risk of acquiring a bloodborne pathogen. PWID who later acquire HCV accumulate more non-pathogenic viruses in plasma than matched controls who do not acquire HCV infection. Additionally, phylogenetic analysis of those non-pathogenic virus sequences reveals drug use networks. Here we find first in Baltimore and confirm in San Francisco that the accumulation of non-pathogenic viruses in PWID is a harbinger for subsequent acquisition of pathogenic viruses, knowledge that may guide the prioritization of the public health resources to combat HIV and HCV.}, }
@article {pmid33563544, year = {2021}, author = {Liwinski, T and Leshem, A and Elinav, E}, title = {Breakthroughs and Bottlenecks in Microbiome Research.}, journal = {Trends in molecular medicine}, volume = {27}, number = {4}, pages = {298-301}, doi = {10.1016/j.molmed.2021.01.003}, pmid = {33563544}, issn = {1471-499X}, mesh = {Diet ; Fecal Microbiota Transplantation ; Host Microbial Interactions ; Humans ; Metagenomics/methods ; *Microbiota/drug effects/genetics/immunology ; Phage Therapy ; Precision Medicine/trends ; Probiotics ; }, abstract = {Over the past 15 years, the research community has witnessed unprecedented progress in microbiome research. We review this increasing knowledge and first attempts of its clinical application, and also limitations and challenges faced by the research community, in mechanistically understanding host-microbiome interactions and integrating these insights into clinical practice.}, }
@article {pmid33397413, year = {2021}, author = {Chen, NC and Solomon, B and Mun, T and Iyer, S and Langmead, B}, title = {Reference flow: reducing reference bias using multiple population genomes.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {8}, pmid = {33397413}, issn = {1474-760X}, support = {R01 HG011392/HG/NHGRI NIH HHS/United States ; R01 GM118568/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromosomes, Human, Pair 21 ; *Genome, Human ; Humans ; *Metagenomics ; Sequence Alignment ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {Most sequencing data analyses start by aligning sequencing reads to a linear reference genome, but failure to account for genetic variation leads to reference bias and confounding of results downstream. Other approaches replace the linear reference with structures like graphs that can include genetic variation, incurring major computational overhead. We propose the reference flow alignment method that uses multiple population reference genomes to improve alignment accuracy and reduce reference bias. Compared to the graph aligner vg, reference flow achieves a similar level of accuracy and bias avoidance but with 14% of the memory footprint and 5.5 times the speed.}, }
@article {pmid34969161, year = {2021}, author = {Wang, L and Yao, H and Tong, T and Lau, K and Leung, SY and Ho, JWK and Leung, WK}, title = {Dynamic changes in antibiotic resistance genes and gut microbiota after Helicobacter pylori eradication therapies.}, journal = {Helicobacter}, volume = {}, number = {}, pages = {e12871}, doi = {10.1111/hel.12871}, pmid = {34969161}, issn = {1523-5378}, support = {//Hong Kong Jockey Club/ ; }, abstract = {BACKGROUND: Short-term antibiotics exposure is associated with alterations in microbiota and antibiotic resistance genes (ARGs) in the human gut. While antibiotics are critical in the successful eradication of Helicobacter pylori, the short-term and long-term impacts on the composition and quantity of antibiotics resistance genes after H. pylori eradication are unclear. This study used whole-genome shotgun metagenomic of stool samples to characterize the gut microbiota and ARGs, before and after H. pylori eradication therapy.<br><br>RESULTS: Forty-four H. pylori-infected patients were recruited, including 21 treatment naïve patients who received clarithromycin-based triple therapy (CLA group) and 23 patients who failed previous therapies, in which 10 received levofloxacin-based quadruple therapy (LEVO group) and 13 received other combinations (OTHER group). Stool samples were collected at baseline (before current treatment), 6 week and 6 month after eradication therapy. At baseline, there was only a slight difference among the three groups on ARGs and gut microbiota. After eradication therapy, there was a transient but significant increase in gut ARGs 6 week post-therapy, among which the LEVO group had the most significant ARGs alteration compared to other two groups. For treatment naïve patients, those with higher ErmF abundance were prone to fail CLA eradication and gain more ARGs after treatment. For gut microbiota, the bacteria richness decreased at 6 week and there was a significant difference in microbiota community among the three groups at 6 week.<br><br>CONCLUSIONS: Our findings demonstrated the dynamic alterations in gut microbiota and ARGs induced by different eradication therapies, which could influence the choices of antibiotics in eradication therapy.}, }
@article {pmid34969117, year = {2021}, author = {Rodino, KG and Pritt, BS}, title = {Novel Applications of Metagenomics for Detection of Tickborne Pathogens.}, journal = {Clinical chemistry}, volume = {68}, number = {1}, pages = {69-74}, doi = {10.1093/clinchem/hvab228}, pmid = {34969117}, issn = {1530-8561}, abstract = {BACKGROUND: Tick populations have expanded in many parts of the globe, bringing with them an enhanced appreciation and discovery of novel tickborne pathogens, as well an increased in reported human cases of tickborne disease. Targeted and unbiased (shotgun) clinical metagenomic sequencing tests are increasingly used for detection of known and emerging infectious agents and have recently been employed for detection of tickborne pathogens.<br><br>CONTENT: This review describes the types of metagenomic sequencing assays used for detection of emerging tickborne pathogens and reviews the recent literature on this topic. Important diagnostic and interpretative challenges are also covered.<br><br>SUMMARY: Metagenomic analysis has emerged as a powerful tool for detection, discovery, characterization, and classification of tickborne pathogens. Shotgun metagenomics is especially promising because it allows for detection of all tickborne bacteria, viruses, and parasites in a single specimen. Despite the potential advantages, there are several important challenges, including high cost, complexity of testing and interpretation, and slow turnaround time. No doubt, these challenges will diminish with increased use and advances in the field.}, }
@article {pmid34969106, year = {2021}, author = {Miller, S and Chiu, C}, title = {The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis.}, journal = {Clinical chemistry}, volume = {68}, number = {1}, pages = {115-124}, doi = {10.1093/clinchem/hvab173}, pmid = {34969106}, issn = {1530-8561}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) for pathogen detection is becoming increasingly available as a method to identify pathogens in cases of suspected infection. mNGS analyzes the nucleic acid content of patient samples with high-throughput sequencing technologies to detect and characterize microorganism DNA and/or RNA. This unbiased approach to organism detection enables diagnosis of a broad spectrum of infection types and can identify more potential pathogens than any single conventional test. This can lead to improved ability to diagnose patients, although there remains concern regarding contamination and detection of nonclinically significant organisms.<br><br>CONTENT: We describe the laboratory approach to mNGS testing and highlight multiple considerations that affect diagnostic performance. We also summarize recent literature investigating the diagnostic performance of mNGS assays for a variety of infection types and recommend further studies to evaluate the improvement in clinical outcomes and cost-effectiveness of mNGS testing.<br><br>SUMMARY: The majority of studies demonstrate that mNGS has sensitivity similar to specific PCR assays and will identify more potential pathogens than conventional methods. While many of these additional organism detections correlate with the expected pathogen spectrum based on patient presentations, there are relatively few formal studies demonstrating whether these are true-positive infections and benefits to clinical outcomes. Reduced specificity due to contamination and clinically nonsignificant organism detections remains a major concern, emphasizing the importance of careful interpretation of the organism pathogenicity and potential association with the clinical syndrome. Further research is needed to determine the possible improvement in clinical outcomes and cost-effectiveness of mNGS testing.}, }
@article {pmid34968878, year = {2021}, author = {Wang, H and Fan, Y and Zhou, M and Wang, W and Li, X and Wang, Y}, title = {Function of Fe(III)-minerals in the enhancement of anammox performance exploiting integrated network and metagenomics analyses.}, journal = {Water research}, volume = {210}, number = {}, pages = {117998}, doi = {10.1016/j.watres.2021.117998}, pmid = {34968878}, issn = {1879-2448}, abstract = {Iron is a recognized physiological requirement for microorganisms but, for anaerobic ammonium oxidation (anammox) bacteria, its role extends well beyond that of a nutritional necessity. In this study, the function of two typical Fe(III)-minerals (ferrihydrite and magnetite) in anammox processes was evaluated in the absence/presence of Fe(II) by integrated network and metagenomics analyses. Results showed that Fe-(III) minerals addition increased the activity of cellular processes and pathways associated with granule formation, enabling the peak values of particle size to increase by 144% and 115%, respectively. Notably, ferrihydrite (5 mM) enhanced nitrogen removal by 4.8% and 4.1%, respectively, in the short-term and long-term absence of Fe(II). Ferrihydrite also promoted the retention of anammox bacteria affiliated with phylum Planctomycetes in the reactor, contributing to an 11% higher abundance with ferrihydrite amendment when compared with the control (without iron additions) in the short-term absence of Fe(II). Network-based analyses revealed that ferrihydrite facilitated the microbial community to form densely clustered and complex topologies to improve resistance to environmental disturbance (i.e., Fe(II) deficiency), and effectively increased the underlying cooperation and facilitation in the community. Metagenomic analysis revealed that there was limited promotion of anammox central metabolism by the extra addition of Fe(III)-minerals in the presence of Fe(II), highlighting the poor utilization of Fe(III)-minerals by anammox bacteria under Fe(II) sufficiency. This study deepens our understanding of the function of Fe(III)-minerals in anammox systems at the community and functional level, and provides a fundamental basis for developing Fe-based anammox enhancement technologies.}, }
@article {pmid34968606, year = {2021}, author = {Varghese, VK and Poddar, BJ and Shah, MP and Purohit, HJ and Khardenavis, AA}, title = {A comprehensive review on current status and future perspectives of microbial volatile fatty acids production as platform chemicals.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152500}, doi = {10.1016/j.scitotenv.2021.152500}, pmid = {34968606}, issn = {1879-1026}, abstract = {Volatile fatty acids (VFA), the secondary metabolite of microbial fermentation, are used in a wide range of industries for production of commercially valuable chemicals. In this review, the fermentative production of VFAs by both pure as well mixed microbial cultures is highlighted along with the strategies for enhancing the VFA production through innovations in existing approaches. Role of conventionally applied tools for the optimization of operational parameters such as pH, temperature, retention time, organic loading rate, and headspace pressure has been discussed. Furthermore, a comparative assessment of above strategies on VFA production has been done with alternate developments such as co-fermentation, substrate pre-treatment, and in situ removal from fermented broth. The review also highlights the applications of different bioreactor geometries in the optimum production of VFAs and how metagenomic tools could provide a detailed insight into the microbial communities and their functional attributes that could be subjected to metabolic engineering for the efficient production of VFAs.}, }
@article {pmid34968587, year = {2021}, author = {Wang, D and Huang, K and He, X and Zhang, XX and Meng, Y}, title = {Varied interspecies interactions between anammox and denitrifying bacteria enhanced nitrogen removal in a single-stage simultaneous anammox and denitrification system.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152519}, doi = {10.1016/j.scitotenv.2021.152519}, pmid = {34968587}, issn = {1879-1026}, abstract = {The simultaneous anammox and denitrification (SAD) system has received growing interest for the enhanced nitrogen removal, while the ecological traits of microbial community including spatial distribution characteristics, assembly processes and interspecies interactions have not been fully unraveled. The present study applied metagenomics and ecological analysis methods to gain the ecological traits of microbial communities in the SAD system across different organic substrate loadings. Results showed that organic matter significantly affected the bioreactor performance, and the optimal total nitrogen removal efficiency reached 93.4 ± 0.7% under the COD concentrations of 180 ± 18.2 mg/L. Functional organisms including Candidatus Brocadia (3.9%), Denitratisoma (1.6%), Dokdonella (4.4%) and Thauera (4.6%) obviously enriched under the optimal organic loading conditions. Moreover, microbial communities were significantly governed by deterministic process under high organic concentrations, and the denitrifying organisms displayed important ecological roles in the communities. Although anammox bacteria obviously enriched at the middle of bioreactor, it possessed the highest expression activities at both bottom and middle sites. Denitrifying bacteria that enriched at the bottom sites strongly achieved nitrate reduction and provided nitrite for anammox bacteria, while these organisms trended to compete nitrite with anammox bacteria at the middle site. These findings highlight the importance of microbial ecology in the SAD systems, which may expand our understanding of the synergistic patterns between anammox and denitrifying bacteria.}, }
@article {pmid34965016, year = {2021}, author = {Yu, JS and Youn, GS and Choi, J and Kim, CH and Kim, BY and Yang, SJ and Lee, JH and Park, TS and Kim, BK and Kim, YB and Roh, SW and Min, BH and Park, HJ and Yoon, SJ and Lee, NY and Choi, YR and Kim, HS and Gupta, H and Sung, H and Han, SH and Suk, KT and Lee, DY}, title = {Lactobacillus lactis and Pediococcus pentosaceus-driven reprogramming of gut microbiome and metabolome ameliorates the progression of non-alcoholic fatty liver disease.}, journal = {Clinical and translational medicine}, volume = {11}, number = {12}, pages = {e634}, doi = {10.1002/ctm2.634}, pmid = {34965016}, issn = {2001-1326}, abstract = {BACKGROUND: Although microbioa-based therapies have shown putative effects on the treatment of non-alcoholic fatty liver disease (NAFLD), it is not clear how microbiota-derived metabolites contribute to the prevention of NAFLD. We explored the metabolomic signature of Lactobacillus lactis and Pediococcus pentosaceus in NAFLD mice and its association in NAFLD patients.<br><br>METHODS: We used Western diet-induced NAFLD mice, and L. lactis and P. pentosaceus were administered to animals in the drinking water at a concentration of 109 CFU/g for 8 weeks. NAFLD severity was determined based on liver/body weight, pathology and biochemistry markers. Caecal samples were collected for the metagenomics by 16S rRNA sequencing. Metabolite profiles were obtained from caecum, liver and serum. Human stool samples (healthy control [n = 22] and NAFLD patients [n = 23]) were collected to investigate clinical reproducibility for microbiota-derived metabolites signature and metabolomics biomarker.<br><br>RESULTS: L. lactis and P. pentosaceus supplementation effectively normalized weight ratio, NAFLD activity score, biochemical markers, cytokines and gut-tight junction. While faecal microbiota varied according to the different treatments, key metabolic features including short chain fatty acids (SCFAs), bile acids (BAs) and tryptophan metabolites were analogously restored by both probiotic supplementations. The protective effects of indole compounds were validated with in vitro and in vivo models, including anti-inflammatory effects. The metabolomic signatures were replicated in NAFLD patients, accompanied by the comparable levels of Firmicutes/Bacteroidetes ratio, which was significantly higher (4.3) compared with control (0.6). Besides, the consequent biomarker panel with six stool metabolites (indole, BAs, and SCFAs) showed 0.922 (area under the curve) in the diagnosis of NAFLD.<br><br>CONCLUSIONS: NAFLD progression was robustly associated with metabolic dys-regulations in the SCFAs, bile acid and indole compounds, and NAFLD can be accurately diagnosed using the metabolites. L. lactis and P. pentosaceus ameliorate NAFLD progression by modulating gut metagenomic and metabolic environment, particularly tryptophan pathway, of the gut-liver axis.}, }
@article {pmid34964882, year = {2021}, author = {Wei, J and Zhang, C and Gao, Y and Li, Y and Zhang, Q and Qi, H and Jin, M and Yang, X and Su, X and Zhang, Y and Yang, R}, title = {Gut Epithelial-derived CXCL9 Maintains Gut Homeostasis through Preventing Overgrown E. coli.}, journal = {Journal of Crohn's &amp; colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjab234}, pmid = {34964882}, issn = {1876-4479}, abstract = {BACKGROUND AND AIMS: The increased E. coli in colon are related to the occurrence and development of multiple diseases. Chemokines are shown to possess potentially antimicrobial activity, including Gram positive and negative bacterial pathogens. We here investigated function(s) of chemokine CXCL9 expressed in the gut epithelial cells and mechanism(s) of CXCL9 to kill E. coli.<br><br>METHODS: We generated CXCL9 fl/flpvillin-cre T mice (pvillin-cre positive mice) and their control CXCL9 fl/flpvillin-cre wmice (pvillin-cre negative mice), and then employed dextran sulfate sodium (DSS)-mediated colitis model to determine sensitivity of the CXCL9 fl/flpvillin-cre T mice. We analyzed composition of the gut microbiota by using 16S ribosomal RNA (V3-V4 variable region) sequencing and shotgun metagenomic analyses. We generated E. coli ∆FtsX (FtsX depleted E. coli) and E. coli ∆aceE (aceE depleted E. coli) by using bacterium red recombining system to investigate the mechanism(s) of CXCL9 to kill E. coli.<br><br>RESULTS: CXCL9 fl/flpvillin-cre Tmice were more sensitive to chemically induced colitis than their control littermates CXCL9 fl/flpvillin-cre wmice. After DSS treatment, there were markedly increased gut E. coli (Escherichia-Shigella) in the colonic contents of CXCL9 fl/flpvillin-cre T mice as compared to control CXCL9 fl/flpvillin-cre w mice. The increased E. coli could promote colitis through NLRC4 and caspase 1/11-mediated IL-18, which was derived from gut epithelial cells. We finally demonstrated that CXCL9 expressed in gut epithelial cells could kill the overgrown E. coli. E. coli expressed Ftsx and PDHc subunits aceE. E.coli∆aceE but not E. coli∆FtsX were resistant to CXCL9-mediated killing.<br><br>CONCLUSIONS: Gut epithelial cells-derived CXCL9 can kill the expanded E. coli through aceE to remain gut homeostasis.}, }
@article {pmid34964297, year = {2021}, author = {Becsei, Á and Solymosi, N and Csabai, I and Magyar, D}, title = {Detection of antimicrobial resistance genes in urban air.}, journal = {MicrobiologyOpen}, volume = {10}, number = {6}, pages = {e1248}, doi = {10.1002/mbo3.1248}, pmid = {34964297}, issn = {2045-8827}, support = {874735//H2020- SC1-BHC-13-2019/ ; }, abstract = {To understand antibiotic resistance in pathogenic bacteria, we need to monitor environmental microbes as reservoirs of antimicrobial resistance genes (ARGs). These bacteria are present in the air and can be investigated with the whole metagenome shotgun sequencing approach. This study aimed to investigate the feasibility of a method for metagenomic analysis of microbial composition and ARGs in the outdoor air. Air samples were collected with a Harvard impactor in the PM10 range at 50 m from a hospital in Budapest. From the DNA yielded from samples of PM10 fraction single-end reads were generated with an Ion Torrent sequencer. During the metagenomic analysis, reads were classified taxonomically. The core bacteriome was defined. Reads were assembled to contigs and the ARG content was analyzed. The dominant genera in the core bacteriome were Bacillus, Acinetobacter, Leclercia and Paenibacillus. Among the identified ARGs best hits were vanRA, Bla1, mphL, Escherichia coli EF-Tu mutants conferring resistance to pulvomycin; BcI, FosB, and mphM. Despite the low DNA content of the samples of PM10 fraction, the number of detected airborne ARGs was surprisingly high.}, }
@article {pmid34964273, year = {2021}, author = {Takizawa, S and Asano, R and Fukuda, Y and Baba, Y and Tada, C and Nakai, Y}, title = {Shifts in xylanases and the microbial community associated with xylan biodegradation during treatment with rumen fluid.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.13988}, pmid = {34964273}, issn = {1751-7915}, support = {JP17H01512//Japan Society for the Promotion of Science/ ; JP19J12745//Japan Society for the Promotion of Science/ ; JP21H04749//Japan Society for the Promotion of Science/ ; //A-STEP/ ; //Miyagi Prefectural Government Recycling Promotion Division/ ; //Miyagi Organization for Industry Promotion/ ; }, abstract = {Treatment with rumen fluid improves methane production from non-degradable lignocellulosic biomass during subsequent methane fermentation; however, the kinetics of xylanases during treatment with rumen fluid remain unclear. This study aimed to identify key xylanases contributing to xylan degradation and their individual activities during xylan treatment with bovine rumen microorganisms. Xylan was treated with bovine rumen fluid at 37°C for 48 h under anaerobic conditions. Total solids were degraded into volatile fatty acids and gases during the first 24 h. Zymography showed that xylanases of 24, 34, 85, 180, and 200 kDa were highly active during the first 24 h. Therefore, these xylanases are considered to be crucial for xylan degradation during treatment with rumen fluid. Metagenomic analysis revealed that the rumen microbial community's structure and metabolic function temporally shifted during xylan biodegradation. Although statistical analyses did not reveal significantly positive correlations between xylanase activities and known xylanolytic bacterial genera, they positively correlated with protozoal (e.g., Entodinium, Diploplastron, and Eudiplodinium) and fungal (e.g., Neocallimastix, Orpinomyces, and Olpidium) genera and unclassified bacteria. Our findings suggest that rumen protozoa, fungi, and unclassified bacteria are associated with key xylanase activities, accelerating xylan biodegradation into volatile fatty acids and gases, during treatment of lignocellulosic biomass with rumen fluid.}, }
@article {pmid34963581, year = {2021}, author = {Caravaca, F and Torres, P and Díaz, G and Roldán, A}, title = {Elevated functional versatility of the soil microbial community associated with the invader Carpobrotus edulis across a broad geographical scale.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152627}, doi = {10.1016/j.scitotenv.2021.152627}, pmid = {34963581}, issn = {1879-1026}, abstract = {Exotic invasive plants may shape their own rhizosphere microbial community during global invasions. Nevertheless, the impacts of such plant invasions on the functional capacities of soil microbial communities remain poorly explored. We used an approach at a broad geographical scale to estimate the composition and abundance of the fungal functional groups, as well as the bacterial metabolic functions, associated with the rhizospheres of Carpobrotus edulis (L.) L. Bolus and the predominant native plants in coastal ecosystems located in different geographical regions. We used the ASV method to infer the potential functions of the soil microbial community with the PICRUSt2 and FUNGuild tools. The predictive functional profiling of the bacterial communities differed between the rhizospheres of the invasive and native plants, regardless of the biogeographic location of the invaded soil. Some predicted pathways related to the biosynthesis of nucleotides such as ppGpp and pppGpp, lipids, carbohydrates and secondary metabolites and the degradation of organic matter were enriched in the C. edulis rhizosphere. Moreover, the invasive microbiota was characterised by a greater richness and diversity of catabolic enzymes involved in nutrients cycling and higher relative abundances of saprotrophs and pathotrophs. Invasion by C. edulis promoted a shift in the potential functional versatility of the soil microbial communities, which can cope with nutrient limitations and biotic stress, and can favour the establishment of the invasive plant, but also alter the functioning and stability of the invaded ecosystems.}, }
@article {pmid34963542, year = {2022}, author = {Chen, J and Yang, Y and Jiang, X and Ke, Y and He, T and Xie, S}, title = {Metagenomic insights into the profile of antibiotic resistomes in sediments of aquaculture wastewater treatment system.}, journal = {Journal of environmental sciences (China)}, volume = {113}, number = {}, pages = {345-355}, doi = {10.1016/j.jes.2021.06.026}, pmid = {34963542}, issn = {1001-0742}, abstract = {To meet the rapidly growing global demand for aquaculture products, large amounts of antibiotics were used in aquaculture, which might accelerate the evolution of antibiotic-resistant bacteria (ARB) and the propagation of antibiotic genes (ARGs). In our research, we revealed the ARGs profiles, their co-occurrence with mobile genetic elements (MGEs), and potential hosts in sediments of a crab pond wastewater purification system based on metagenomic analysis. The residual antibiotic seems to increase the propagation of ARGs in the crab pond, but there was no clear relationship between a given antibiotic type and the corresponding resistance genes. The effect of aquaculture on sediment was not as profound as that of other anthropogentic activities, but increased the relative abundance of sulfonamide resistance gene. A higher abundance of MGEs, especially plasmid, increased the potential ARGs dissemination risk in crab and purification ponds. Multidrug and sulfonamide resistance genes had greater potential to transfer because they were more frequently carried by MGEs. The horizontal gene transfer was likely to occur among a variety of microorganisms, and various ARGs hosts including Pseudomonas, Acinetobacter, Escherichia, and Klebsiella were identified. Bacterial community influenced the composition of ARG hosts, and Proteobacteria was the predominant hosts. Overall, our study provides novel insights into the environmental risk of ARGs in sediments of aquaculture wastewater treatment system.}, }
@article {pmid34963452, year = {2021}, author = {Lin, H and Guo, Q and Wen, Z and Tan, S and Chen, J and Lin, L and Chen, P and He, J and Wen, J and Chen, Y}, title = {The multiple effects of fecal microbiota transplantation on diarrhea-predominant irritable bowel syndrome (IBS-D) patients with anxiety and depression behaviors.}, journal = {Microbial cell factories}, volume = {20}, number = {1}, pages = {233}, pmid = {34963452}, issn = {1475-2859}, support = {No. 81770529//National Natural Science Foundation of China/ ; No. 82070543//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Anxiety and depression are complications in Irritable bowel syndrome (IBS) patients. In this study, we recruited 18 IBS patients with mild-modest anxiety and depression behaviors, and after the screening, we defined the FMT treatment group (n = 9) and the control group (n = 9). The IBS symptom severity scale (IBS-SSS), Hamilton Anxiety Rating Scale (HAM-A), Hamilton Depression Rating Scale (HAM-D), Irritable Bowel Syndrome Quality of Life (IBS-QOL) and Bristol stool scale (BSS) were evaluated one week before FMT (baseline), one-week-, one-month-, two-month-, and three-month-following FMT. Meanwhile, we determined the SCFAs in the patient's feces and serum and continued the metagenomic analysis of the microorganisms in the patient's feces.<br><br>RESULTS: The results showed that the patient's anxiety and depression behavior gradually improved with FMT treatment. Moreover, the illness and quality of life had also been relieved significantly. The content of isovaleric acid and valeric acid was significantly reduced in the FMT group compared to the Col group. Metagenomic analysis showed that FMT treatment decreased the abundance of Faecalibacterium, Eubacterium and Escherichia. From KEGG functional analysis, we confirmed that the top five abundant pathways were "bacterial chemotaxis, "flagellar assembly", "glycine, serine and threonine metabolism", "apoptosis", and "bacterial invasion of epithelial cells".<br><br>CONCLUSIONS: FMT treatment can effectively alleviate the anxiety and depression behaviors of IBS-D patients and reduce the IBS-SSS score, indicating that FMT can improve patients' symptoms. The high throughput sequencing results show that Bifidobacterium and Escherichia play the most critical role in the formation and recovery of IBS-D patients. The GC/MS data indicated that faeces isovaleric acid and valeric acid might be more suitable as a metabolic indicator of IBS-D remission. Trial registration ChiCTR, ChiCTR1900024924, Registered 3 August 2019, https://www.chictr.org.cn/showproj.aspx?proj=41676 .}, }
@article {pmid33952388, year = {2021}, author = {Chen, YH and Yang, SH and Tandon, K and Lu, CY and Chen, HJ and Shih, CJ and Tang, SL}, title = {Potential syntrophic relationship between coral-associated Prosthecochloris and its companion sulfate-reducing bacterium unveiled by genomic analysis.}, journal = {Microbial genomics}, volume = {7}, number = {5}, pages = {}, pmid = {33952388}, issn = {2057-5858}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/metabolism ; Chlorobi/*classification/*genetics/*metabolism ; DNA, Bacterial/genetics ; Desulfovibrionaceae ; Genome ; *Genomics ; Metagenome ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates/*metabolism ; }, abstract = {Endolithic microbial symbionts in the coral skeleton may play a pivotal role in maintaining coral health. However, compared to aerobic micro-organisms, research on the roles of endolithic anaerobic micro-organisms and microbe-microbe interactions in the coral skeleton are still in their infancy. In our previous study, we showed that a group of coral-associated Prosthecochloris (CAP), a genus of anaerobic green sulphur bacteria, was dominant in the skeleton of the coral Isopora palifera. Though CAP is diverse, the 16S rRNA phylogeny presents it as a distinct clade separate from other free-living Prosthecochloris. In this study, we build on previous research and further characterize the genomic and metabolic traits of CAP by recovering two new high-quality CAP genomes - Candidatus Prosthecochloris isoporae and Candidatus Prosthecochloris sp. N1 - from the coral I. palifera endolithic cultures. Genomic analysis revealed that these two CAP genomes have high genomic similarities compared with other Prosthecochloris and harbour several CAP-unique genes. Interestingly, different CAP species harbour various pigment synthesis and sulphur metabolism genes, indicating that individual CAPs can adapt to a diversity of coral microenvironments. A novel high-quality genome of sulfate-reducing bacterium (SRB)- Candidatus Halodesulfovibrio lyudaonia - was also recovered from the same culture. The fact that CAP and various SRB co-exist in coral endolithic cultures and coral skeleton highlights the importance of SRB in the coral endolithic community. Based on functional genomic analysis of Ca. P. sp. N1, Ca. P. isoporae and Ca. H. lyudaonia, we also propose a syntrophic relationship between the SRB and CAP in the coral skeleton.}, }
@article {pmid34962589, year = {2021}, author = {Kalu, CM and Ogola, HJO and Selvarajan, R and Tekere, M and Ntushelo, K}, title = {Correlations Between Root Metabolomics and Bacterial Community Structures in the Phragmites australis Under Acid Mine Drainage-Polluted Wetland Ecosystem.}, journal = {Current microbiology}, volume = {79}, number = {1}, pages = {34}, pmid = {34962589}, issn = {1432-0991}, support = {129095//national research foundation/ ; }, abstract = {Despite root microecology playing critical role in plant growth and fidelity, relatively few studies have focused on the link between the microbial communities and root metabolome in the aquatic macrophytes under heavy metal (HM) pollution. Using high-throughput metagenomic sequencing, targeted metabolomics and community-level physiological profile analyses, we investigated the symbiotic associations between Phragmites australis with rhizospheric bacterial communities under differing acid mine drainage (AMD) pollution. Results indicated that AMD pollution and root localization significantly affected root metabolome profiles. Higher accumulation of adenosine monophosphate, inosine, methionine, carnitine and dimethylglycine were observed in the rhizosphere under AMD than non-AMD habitat. Overall, the bacterial diversity and richness, and functional (metabolic) diversity were lower under high-AMD pollution. While non-AMD site was enriched with members of phylum Firmicutes, Proteobacteria were the most abundant taxa in the rhizosphere and endosphere under AMD-polluted sites. Further, plant growth promoting rhizobacteria (Rhizobium, Delftia, Bradyrhizobium, and Mesorhizobium) and metal-tolerant bacteria (Bacillus, Arthrobacter, Massilia and Methylocystis) were most abundant in AMD-polluted than non-AMD habitat. Finally, pH, TDS (total dissolved solids), Cu, Cr, Fe, and Zn content were the key environmental factors that strongly contributed to the spatial perturbation of rhizospheric metabolites, proteobacterial and acidobacterial taxa. Overall, the study linked the differential endospheric and rhizospheric bacterial community and metabolite profiles in P. australis under AMD environment and provided insights into HM adaptability and phytoremediation potential.}, }
@article {pmid34962473, year = {2021}, author = {Yu, J and Wu, R and Xiong, B and Huang, Z and Li, H}, title = {Metagenomic Next-Generation Sequencing in the Diagnosis of Deep Sternal Wound Infection After Cardiac Transplantation: A Case Report and Literature Review.}, journal = {The heart surgery forum}, volume = {24}, number = {6}, pages = {E1015-E1017}, doi = {10.1532/hsf.4169}, pmid = {34962473}, issn = {1522-6662}, abstract = {PURPOSE: To explore the value of metagenomics next-generation sequencing (mNGS) for deep sternal wound infection (DSWI) diagnosis.<br><br>METHODS: mNGS was used to diagnose DSWI after cardiac transplantation; DSWI was treated with surgical debridement, wound care, and antibiotic therapy guided by mNGS.<br><br>RESULTS: Coinfection of methicillin-resistant Staphylococcus aureus (MRSA) and cytomegalovirus (CMV) was detected in this patient. The infection was controlled and the wound healed successfully with the specific medicine based on mNGS results for 3 weeks.<br><br>CONCLUSION: mNGS is effective to achieve precise, individualized, and rapid treatment for wound infection.}, }
@article {pmid34962421, year = {2021}, author = {Xiao, K and Zhao, D and Luo, Y and Si, Y}, title = {Streptococcus constellatus Causing Brain Abscess Identified by Metagenomics Next-Generation Sequencing.}, journal = {Surgical infections}, volume = {}, number = {}, pages = {}, doi = {10.1089/sur.2021.338}, pmid = {34962421}, issn = {1557-8674}, }
@article {pmid34962128, year = {2021}, author = {Seo, S and Disney-McKeethen, S and Prabhakar, RG and Song, X and Mehta, HH and Shamoo, Y}, title = {Identification of Evolutionary Trajectories Associated with Antimicrobial Resistance Using Microfluidics.}, journal = {ACS infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsinfecdis.1c00564}, pmid = {34962128}, issn = {2373-8227}, abstract = {In vitro experimental evolution of pathogens to antibiotics is commonly used for the identification of clinical biomarkers associated with antibiotic resistance. Microdroplet emulsions allow exquisite control of spatial structure, species complexity, and selection microenvironments for such studies. We investigated the use of monodisperse microdroplets in experimental evolution. Using Escherichia coli adaptation to doxycycline, we examined how changes in environmental conditions such as droplet size, starting lambda value, selection strength, and incubation method affected evolutionary outcomes. We also examined the extent to which emulsions could reveal potentially new evolutionary trajectories and dynamics associated with antimicrobial resistance. Interestingly, we identified both expected and unexpected evolutionary trajectories including large-scale chromosomal rearrangements and amplification that were not observed in suspension culture methods. As microdroplet emulsions are well-suited for automation and provide exceptional control of conditions, they can provide a high-throughput approach for biomarker identification as well as preclinical evaluation of lead compounds.}, }
@article {pmid34961896, year = {2021}, author = {Johny, TK and Puthusseri, RM and Bhat, SG}, title = {Metagenomic landscape of taxonomy, metabolic potential and resistome of Sardinella longiceps gut microbiome.}, journal = {Archives of microbiology}, volume = {204}, number = {1}, pages = {87}, pmid = {34961896}, issn = {1432-072X}, support = {MOES/10-MLR/2/2007//centre for marine living resources &amp; ecology- ministry of earth sciences, government of india/ ; MOES/10-MLRTD/03/2013//centre for marine living resources &amp; ecology- ministry of earth sciences, government of india/ ; }, abstract = {Fish gut microbiota, encompassing a colossal reserve of microbes represents a dynamic ecosystem, influenced by a myriad of environmental and host factors. The current study presents a comprehensive insight into Sardinella longiceps gut microbiome using whole metagenome shotgun sequencing. Taxonomic profiling identified the predominance of phylum Proteobacteria, comprising of Photobacterium, Vibrio and Shewanella sp. Functional annotation revealed the dominance of Clustering based subsystems, Carbohydrate, and Amino acids and derivatives. Analysis of Virulence, disease and defense subsystem identified genes conferring resistance to antibiotics and toxic compounds, like multidrug resistance efflux pumps and resistance genes for fluoroquinolones and heavy metals like cobalt, zinc, cadmium and copper. The presence of overlapping genetic mechanisms of resistance to antibiotics and heavy metals, like the efflux pumps is a serious cause of concern as it is likely to aggravate co-selection pressure, leading to an increased dissemination of these resistance genes to fish and humans.}, }
@article {pmid34961295, year = {2021}, author = {Juurakko, CL and diCenzo, GC and Walker, VK}, title = {Cold Acclimation in Brachypodium Is Accompanied by Changes in Above-Ground Bacterial and Fungal Communities.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/plants10122824}, pmid = {34961295}, issn = {2223-7747}, support = {Dr. Virginia Walker//Natural Sciences and Engineering Research Council/ ; Dr. George diCenzo//Queen's University/ ; }, abstract = {Shifts in microbiota undoubtedly support host plants faced with abiotic stress, including low temperatures. Cold-resistant perennials prepare for freeze stress during a period of cold acclimation that can be mimicked by transfer from growing conditions to a reduced photoperiod and a temperature of 4 °C for 2-6 days. After cold acclimation, the model cereal, Brachypodium distachyon, was characterized using metagenomics supplemented with amplicon sequencing (16S ribosomal RNA gene fragments and an internal transcribed spacer region). The bacterial and fungal rhizosphere remained largely unchanged from that of non-acclimated plants. However, leaf samples representing bacterial and fungal communities of the endo- and phyllospheres significantly changed. For example, a plant-beneficial bacterium, Streptomyces sp. M2, increased more than 200-fold in relative abundance in cold-acclimated leaves, and this increase correlated with a striking decrease in the abundance of Pseudomonas syringae (from 8% to zero). This change is of consequence to the host, since P. syringae is a ubiquitous ice-nucleating phytopathogen responsible for devastating frost events in crops. We posit that a responsive above-ground bacterial and fungal community interacts with Brachypodium's low temperature and anti-pathogen signalling networks to help ensure survival in subsequent freeze events, underscoring the importance of inter-kingdom partnerships in the response to cold stress.}, }
@article {pmid34961260, year = {2021}, author = {Stavridou, E and Giannakis, I and Karamichali, I and Kamou, NN and Lagiotis, G and Madesis, P and Emmanouil, C and Kungolos, A and Nianiou-Obeidat, I and Lagopodi, AL}, title = {Biosolid-Amended Soil Enhances Defense Responses in Tomato Based on Metagenomic Profile and Expression of Pathogenesis-Related Genes.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/plants10122789}, pmid = {34961260}, issn = {2223-7747}, support = {MIS-5000432//State Scholarships Foundation/ ; }, abstract = {Biosolid application is an effective strategy, alternative to synthetic chemicals, for enhancing plant growth and performance and improving soil properties. In previous research, biosolid application has shown promising results with respect to tomato resistance against Fusarium oxysporum f. sp. radicis-lycopersici (Forl). Herein, we aimed at elucidating the effect of biosolid application on the plant-microbiome response mechanisms for tomato resistance against Forl at a molecular level. More specifically, plant-microbiome interactions in the presence of biosolid application and the biocontrol mechanism against Forl in tomato were investigated. We examined whether biosolids application in vitro could act as an inhibitor of growth and sporulation of Forl. The effect of biosolid application on the biocontrol of Forl was investigated based on the enhanced plant resistance, measured as expression of pathogen-response genes, and pathogen suppression in the context of soil microbiome diversity, abundance, and predicted functions. The expression of the pathogen-response genes was variably induced in tomato plants in different time points between 12 and 72 h post inoculation in the biosolid-enriched treatments, in the presence or absence of pathogens, indicating activation of defense responses in the plant. This further suggests that biosolid application resulted in a successful priming of tomato plants inducing resistance mechanisms against Forl. Our results have also demonstrated that biosolid application alters microbial diversity and the predicted soil functioning, along with the relative abundance of specific phyla and classes, as a proxy for disease suppression. Overall, the use of biosolid as a sustainable soil amendment had positive effects not only on plant health and protection, but also on growth of non-pathogenic antagonistic microorganisms against Forl in the tomato rhizosphere and thus, on plant-soil microbiome interactions, toward biocontrol of Forl.}, }
@article {pmid34961255, year = {2021}, author = {Tebele, SM and Marks, RA and Farrant, JM}, title = {Two Decades of Desiccation Biology: A Systematic Review of the Best Studied Angiosperm Resurrection Plants.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/plants10122784}, pmid = {34961255}, issn = {2223-7747}, support = {98406//National Research Foundation/ ; }, abstract = {Resurrection plants have an extraordinary ability to survive extreme water loss but still revive full metabolic activity when rehydrated. These plants are useful models to understand the complex biology of vegetative desiccation tolerance. Despite extensive studies of resurrection plants, many details underlying the mechanisms of desiccation tolerance remain unexplored. To summarize the progress in resurrection plant research and identify unexplored questions, we conducted a systematic review of 15 model angiosperm resurrection plants. This systematic review provides an overview of publication trends on resurrection plants, the geographical distribution of species and studies, and the methodology used. Using the Preferred Reporting Items for Systematic reviews and Meta-Analyses protocol we surveyed all publications on resurrection plants from 2000 and 2020. This yielded 185 empirical articles that matched our selection criteria. The most investigated plants were Craterostigma plantagineum (17.5%), Haberlea rhodopensis (13.7%), Xerophyta viscosa (reclassified as X. schlechteri) (11.9%), Myrothamnus flabellifolia (8.5%), and Boea hygrometrica (8.1%), with all other species accounting for less than 8% of publications. The majority of studies have been conducted in South Africa, Bulgaria, Germany, and China, but there are contributions from across the globe. Most studies were led by researchers working within the native range of the focal species, but some international and collaborative studies were also identified. The number of annual publications fluctuated, with a large but temporary increase in 2008. Many studies have employed physiological and transcriptomic methodologies to investigate the leaves of resurrection plants, but there was a paucity of studies on roots and only one metagenomic study was recovered. Based on these findings we suggest that future research focuses on resurrection plant roots and microbiome interactions to explore microbial communities associated with these plants, and their role in vegetative desiccation tolerance.}, }
@article {pmid34960807, year = {2021}, author = {Folgueiras-González, A and van den Braak, R and Deijs, M and Kuller, W and Sietsma, S and Thuring, V and van der Hoek, L and de Groof, A}, title = {Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, doi = {10.3390/v13122538}, pmid = {34960807}, issn = {1999-4915}, support = {721367//Horizon 2020, Marie Skłodowska-Curie Actions/ ; }, abstract = {A commercial pig farm with no history of porcine circovirus 2 (PCV2) or porcine reproductive and respiratory syndrome virus (PRRSV) repeatedly reported a significant reduction in body weight gain and wasting symptoms in approximately 20-30% of the pigs in the period between three and six weeks after weaning. As standard clinical interventions failed to tackle symptomatology, viral metagenomics were used to describe and monitor the enteric virome at birth, 3 weeks, 4 weeks, 6 weeks, and 9 weeks of age. The latter four sampling points were 7 days, 3 weeks, and 6 weeks post weaning, respectively. Fourteen distinct enteric viruses were identified within the herd, which all have previously been linked to enteric diseases. Here we show that wasting is associated with alterations in the enteric virome of the pigs, characterized by: (1) the presence of enterovirus G at 3 weeks of age, followed by a higher prevalence of the virus in wasting pigs at 6 weeks after weaning; (2) rotaviruses at 3 weeks of age; and (3) porcine sapovirus one week after weaning. However, the data do not provide a causal link between specific viral infections and the postweaning clinical problems on the farm. Together, our results offer evidence that disturbances in the enteric virome at the preweaning stage and early after weaning have a determining role in the development of intestinal barrier dysfunctions and nutrient uptake in the postweaning growth phase. Moreover, we show that the enteric viral load sharply increases in the week after weaning in both healthy and wasting pigs. This study is also the first to report the dynamics and co-infection of porcine rotavirus species and porcine astrovirus genetic lineages during the first 9 weeks of the life of domestic pigs.}, }
@article {pmid34960803, year = {2021}, author = {Berg, MG and Forberg, K and Perez, LJ and Luk, KC and Meyer, TV and Cloherty, GA}, title = {Emergence of a Distinct Picobirnavirus Genotype Circulating in Patients Hospitalized with Acute Respiratory Illness.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, doi = {10.3390/v13122534}, pmid = {34960803}, issn = {1999-4915}, abstract = {Picobirnaviruses (PBV) are found in a wide range of hosts and typically associated with gastrointestinal infections in immunocompromised individuals. Here, a divergent PBV genome was assembled from a patient hospitalized for acute respiratory illness (ARI) in Colombia. The RdRp protein branched with sequences previously reported in patients with ARI from Cambodia and China. Sputa from hospitalized individuals (n = 130) were screened by RT-qPCR which enabled detection and subsequent metagenomic characterization of 25 additional PBV infections circulating in Colombia and the US. Phylogenetic analysis of RdRp highlighted the emergence of two dominant lineages linked to the index case and Asian strains, which together clustered as a distinct genotype. Bayesian inference further established capsid and RdRp sequences as both significantly associated with ARI. Various respiratory-tropic pathogens were detected in PBV+ patients, yet no specific bacteria was common among them and four individuals lacked co-infections, suggesting PBV may not be a prokaryotic virus nor exclusively opportunistic, respectively. Competing models for the origin and transmission of this PBV genotype are presented that attempt to reconcile vectoring by a bacterial host with human pathogenicity. A high prevalence in patients with ARI, an ability to reassort, and demonstrated global spread indicate PBV warrant greater public health concern.}, }
@article {pmid34960771, year = {2021}, author = {Delwart, E and Tisza, MJ and Altan, E and Li, Y and Deng, X and Hartigan-O'Connor, DJ and Ardeshir, A}, title = {Idiopathic Chronic Diarrhea in Rhesus Macaques Is Not Associated with Enteric Viral Infections.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, doi = {10.3390/v13122503}, pmid = {34960771}, issn = {1999-4915}, support = {5R01AI123376//National Institute of Allergy and Infectious Diseases/ ; P51OD011107-60/CD/ODCDC CDC HHS/United States ; }, abstract = {While recent changes in treatment have reduced the lethality of idiopathic chronic diarrhea (ICD), this condition remains one of the most common causes of rhesus macaque deaths in non-human primate research centers. We compared the viromes in fecal swabs from 52 animals with late stage ICD and 41 healthy animals. Viral metagenomics targeting virus-like particles was used to identify viruses fecally shed by each animal. Five viruses belonging to the Picornaviridae, one to the Caliciviridae, one to the Parvoviridae, and one to the Adenoviridae families were identified. The fraction of reads matching each viral species was then used to estimate and compare viral loads in ICD cases versus healthy controls. None of the viruses detected in fecal swabs were strongly associated with ICD.}, }
@article {pmid34960726, year = {2021}, author = {Redila, CD and Prakash, V and Nouri, S}, title = {Metagenomics Analysis of the Wheat Virome Identifies Novel Plant and Fungal-Associated Viral Sequences.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, doi = {10.3390/v13122457}, pmid = {34960726}, issn = {1999-4915}, support = {Start-up//Kansas State University/ ; KWC 2020-13//Kansas Wheat Commission/ ; }, abstract = {Wheat viruses including wheat streak mosaic virus, Triticum mosaic virus, and barley yellow dwarf virus cost substantial losses in crop yields every year. Although there have been extensive studies conducted on these known wheat viruses, currently, there is limited knowledge about all components of the wheat (Triticum aestivum L.) virome. Here, we determined the composition of the wheat virome through total RNA deep sequencing of field-collected leaf samples. Sequences were de novo assembled after removing the host reads, and BLASTx searches were conducted. In addition to the documented wheat viruses, novel plant and fungal-associated viral sequences were identified. We obtained the full genome sequence of the first umbra-like associated RNA virus tentatively named wheat umbra-like virus in cereals. Moreover, a novel bi-segmented putative virus tentatively named wheat-associated vipovirus sharing low but significant similarity with both plant and fungal-associated viruses was identified. Additionally, a new putative fungal-associated tobamo-like virus and novel putative Mitovirus were discovered in wheat samples. The discovery and characterization of novel viral sequences associated with wheat is important to determine if these putative viruses may pose a threat to the wheat industry or have the potential to be used as new biological control agents for wheat pathogens either as wild-type or recombinant viruses.}, }
@article {pmid34960693, year = {2021}, author = {Paim, WP and Maggioli, MF and Falkenberg, SM and Ramachandran, A and Weber, MN and Canal, CW and Bauermann, FV}, title = {Virome Characterization in Commercial Bovine Serum Batches-A Potentially Needed Testing Strategy for Biological Products.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, doi = {10.3390/v13122425}, pmid = {34960693}, issn = {1999-4915}, abstract = {Bovine serum has been widely used as a universal supplement in culture media and other applications, including the manufacture of biological products and the production of synthetic meat. Currently, commercial bovine serum is tested for possible viral contaminants following regional guidelines. Regulatory agencies' established tests focused on detecting selected animal origin viruses and are based on virus isolation, immunofluorescence, and hemadsorption assays. However, these tests may fail to detect new or emerging viruses in biological products. High-throughput sequencing is a powerful option since no prior knowledge of the viral targets is required. In the present study, we evaluate the virome of seven commercial batches of bovine serum from Mexico (one batch), New Zealand (two batches), and the United States (four batches) using a specific preparation and enrichment method for pooled samples and sequencing using an Illumina platform. A variety of circular replicase-encoding single-stranded (CRESS) DNA families (Genomoviridae, Circoviridae, and Smacoviridae) was identified. Additionally, CrAssphage, a recently discovered group of bacteriophage correlated with fecal contamination, was identified in 85% of the tested batches. Furthermore, sequences representing viral families with single-stranded DNA (Parvoviridae), double-stranded DNA (Polyomaviridae and Adenoviridae), single-stranded RNA (Flaviviridae, Picornaviridae, and Retroviridae), and double-stranded RNA (Reoviridae) were identified. These results support that high-throughput sequencing associated with viral enrichment is a robust tool and should be considered an additional layer of safety when testing pooled biologicals to detect viral contaminants overlooked by the current testing protocols.}, }
@article {pmid34960681, year = {2021}, author = {Huaman, JL and Pacioni, C and Sarker, S and Doyle, M and Forsyth, DM and Pople, A and Carvalho, TG and Helbig, KJ}, title = {Novel Picornavirus Detected in Wild Deer: Identification, Genomic Characterisation, and Prevalence in Australia.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, doi = {10.3390/v13122412}, pmid = {34960681}, issn = {1999-4915}, support = {PO1-L-002//Centre for Invasive Species Solution/ ; }, abstract = {The use of high-throughput sequencing has facilitated virus discovery in wild animals and helped determine their potential threat to humans and other animals. We report the complete genome sequence of a novel picornavirus identified by next-generation sequencing in faeces from Australian fallow deer. Genomic analysis revealed that this virus possesses a typical picornavirus-like genomic organisation of 7554 nt with a single open reading frame (ORF) encoding a polyprotein of 2225 amino acids. Based on the amino acid identity comparison and phylogenetic analysis of the P1, 2C, 3CD, and VP1 regions, this novel picornavirus was closely related to but distinct from known bopiviruses detected to date. This finding suggests that deer/bopivirus could belong to a novel species within the genus Bopivirus, tentatively designated as "Bopivirus C". Epidemiological investigation of 91 deer (71 fallow, 14 sambar and 6 red deer) and 23 cattle faecal samples showed that six fallow deer and one red deer (overall prevalence 7.7%, 95% confidence interval [CI] 3.8-15.0%) tested positive, but deer/bopivirus was undetectable in sambar deer and cattle. In addition, phylogenetic and sequence analyses indicate that the same genotype is circulating in south-eastern Australia. To our knowledge, this study reports for the first time a deer-origin bopivirus and the presence of a member of genus Bopivirus in Australia. Further epidemiological and molecular studies are needed to investigate the geographic distribution and pathogenic potential of this novel Bopivirus species in other domestic and wild animal species.}, }
@article {pmid34960644, year = {2021}, author = {Litov, AG and Belova, OA and Kholodilov, IS and Gadzhikurbanov, MN and Gmyl, LV and Oorzhak, ND and Saryglar, AA and Ishmukhametov, AA and Karganova, GG}, title = {Possible Arbovirus Found in Virome of Melophagus ovinus.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, doi = {10.3390/v13122375}, pmid = {34960644}, issn = {1999-4915}, support = {21-14-00245//Russian Science Foundation/ ; }, abstract = {Members of the Lipopteninae subfamily are blood-sucking ectoparasites of mammals. The sheep ked (Melophagus ovinus) is a widely distributed ectoparasite of sheep. It can be found in most sheep-rearing areas and can cause skin irritation, restlessness, anemia, weight loss and skin injuries. Various bacteria and some viruses have been detected in M. ovinus; however, the virome of this ked has never been studied using modern approaches. Here, we study the virome of M. ovinus collected in the Republic of Tuva, Russia. In our research, we were able to assemble full genomes for five novel viruses, related to the Rhabdoviridae (Sigmavirus), Iflaviridae, Reoviridae and Solemoviridae families. Four viruses were found in all five of the studied pools, while one virus was found in two pools. Phylogenetically, all of the novel viruses clustered together with various recently described arthropod viruses. All the discovered viruses were tested on their ability to replicate in the mammalian porcine embryo kidney (PEK) cell line. Aksy-Durug Melophagus sigmavirus RNA was detected in the PEK cell line cultural supernate after the first, second and third passages. Such data imply that this virus might be able to replicate in mammalian cells, and thus, can be considered as a possible arbovirus.}, }
@article {pmid34960634, year = {2021}, author = {do Socorro Fôro Ramos, E and de Oliveira Ribeiro, G and Villanova, F and de Padua Milagres, FA and Brustulin, R and Araújo, ELL and Pandey, RP and Raj, VS and Deng, X and Delwart, E and Luchs, A and da Costa, AC and Leal, É}, title = {Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, doi = {10.3390/v13122365}, pmid = {34960634}, issn = {1999-4915}, abstract = {Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples.}, }
@article {pmid34960611, year = {2021}, author = {Happel, AU and Balle, C and Maust, BS and Konstantinus, IN and Gill, K and Bekker, LG and Froissart, R and Passmore, JA and Karaoz, U and Varsani, A and Jaspan, H}, title = {Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents.}, journal = {Viruses}, volume = {13}, number = {12}, pages = {}, doi = {10.3390/v13122341}, pmid = {34960611}, issn = {1999-4915}, support = {R01 HD083040/NH/NIH HHS/United States ; R01 AI094586/NH/NIH HHS/United States ; }, abstract = {The interaction between gut bacterial and viral microbiota is thought to be important in human health. While fluctuations in female genital tract (FGT) bacterial microbiota similarly determine sexual health, little is known about the presence, persistence, and function of vaginal bacteriophages. We conducted shotgun metagenome sequencing of cervicovaginal samples from South African adolescents collected longitudinally, who received no antibiotics. We annotated viral reads and circular bacteriophages, identified CRISPR loci and putative prophages, and assessed their diversity, persistence, and associations with bacterial microbiota composition. Siphoviridae was the most prevalent bacteriophage family, followed by Myoviridae, Podoviridae, Herelleviridae, and Inoviridae. Full-length siphoviruses targeting bacterial vaginosis (BV)-associated bacteria were identified, suggesting their presence in vivo. CRISPR loci and prophage-like elements were common, and genomic analysis suggested higher diversity among Gardnerella than Lactobacillus prophages. We found that some prophages were highly persistent within participants, and identical prophages were present in cervicovaginal secretions of multiple participants, suggesting that prophages, and thus bacterial strains, are shared between adolescents. The number of CRISPR loci and prophages were associated with vaginal microbiota stability and absence of BV. Our analysis suggests that (pro)phages are common in the FGT and vaginal bacteria and (pro)phages may interact.}, }
@article {pmid34960001, year = {2021}, author = {Kaashyap, M and Cohen, M and Mantri, N}, title = {Microbial Diversity and Characteristics of Kombucha as Revealed by Metagenomic and Physicochemical Analysis.}, journal = {Nutrients}, volume = {13}, number = {12}, pages = {}, doi = {10.3390/nu13124446}, pmid = {34960001}, issn = {2072-6643}, abstract = {Kombucha is a fermented tea made from a Symbiotic Culture of Bacteria and Yeast (SCOBY) with a long history of use as a health tonic. It is likely that most health benefits come from the tea and fermentation metabolites from specific microbial communities. Despite its growing importance as a functional health drink, the microbial ecosystem present in kombucha has not been fully documented. To characterize the microbial composition and biochemical properties of 'The Good Brew' original base kombucha, we used metagenomics amplicon (16S rRNA and ITS) sequencing to identify the microbial communities at the taxonomic level. We identified 34 genera with 200 microbial species yet described in kombucha. The dominance of organic acid producing microorganisms Acetobacter, Komagataeibacter and Starmerella are healthy for the human gut and their glucose metabolising activities have a putative role in preventing conditions such as diabetes and obesity. Kombucha contains high protein (3.31 µg/mL), high phenolic content (290.4 mg/100 mL) and low sugars (glucose: 1.87 g/L; sucrose 1.11 g/L; fructose: 0.05 g/L) as compared to green tea. The broad microbial diversity with proven health benefits for the human gut suggests kombucha is a powerful probiotic. These findings are important to improve the commercial value of kombucha and uncover the immense prospects for health benefits.}, }
@article {pmid34959567, year = {2021}, author = {Kovács, C and Csótó, A and Pál, K and Nagy, A and Fekete, E and Karaffa, L and Kubicek, CP and Sándor, E}, title = {The Biocontrol Potential of Endophytic Trichoderma Fungi Isolated from Hungarian Grapevines. Part I. Isolation, Identification and In Vitro Studies.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/pathogens10121612}, pmid = {34959567}, issn = {2076-0817}, support = {NN128867//National Research, Development and Innovation Office/ ; K138489//National Research, Development and Innovation Office/ ; EFOP-3.6.1-16-2016-00022//European Union and the European Social Fund/ ; }, abstract = {This paper reports on the identification and in vitro characterization of several Trichoderma strains isolated from the Tokaj Wine Region in North-East Hungary. Ten isolates were analyzed and found to consist of six individual species-T. gamsii, T. orientale, T. simmonsii, T. afroharzianum, T. atrobrunneum and T. harzianum&amp;nbsp;sensu stricto. The growth potential of the strains was assessed at a range of temperatures. We also report here on the in vitro biocontrol properties and fungicide tolerance of the most promising strains.}, }
@article {pmid34959514, year = {2021}, author = {Sarker, S}, title = {Molecular and Phylogenetic Characterisation of a Highly Divergent Novel Parvovirus (Psittaciform Chaphamaparvovirus 2) in Australian Neophema Parrots.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/pathogens10121559}, pmid = {34959514}, issn = {2076-0817}, abstract = {Parvoviruses under the genus Chaphamaparvovirus (subfamily Hamaparvovirinae) are highly divergent and have recently been identified in many animals. However, the detection and characterisation of parvoviruses in psittacine birds are limited. Therefore, this study reports a novel parvovirus, tentatively named psittaciform chaphamaparvovirus 2 (PsChPV-2) under the genus Chaphamaparvovirus, which was identified in Australian Neophema birds. The PsChPV-2 genome is 4371 bp in length and encompasses four predicted open-reading frames, including two major genes, a nonstructural replicase gene (NS1), and a structural capsid gene (VP1). The NS1 and VP1 genes showed the closest amino acid identities of 56.2% and 47.7%, respectively, with a recently sequenced psittaciform chaphamaparvovirus 1 from a rainbow lorikeet (Trichoglossus moluccanus). Subsequent phylogenetic analyses exhibited that the novel PsChPV-2 is most closely related to other chaphamaparvoviruses of avian origin and has the greatest sequence identity with PsChPV-1 (60.6%). Further systematic investigation is warranted to explore the diversity with many avian-associated parvoviruses likely to be discovered.}, }
@article {pmid34959505, year = {2021}, author = {Pane, S and Ristori, MV and Gardini, S and Russo, A and Del Chierico, F and Putignani, L}, title = {Clinical Parasitology and Parasitome Maps as Old and New Tools to Improve Clinical Microbiomics.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/pathogens10121550}, pmid = {34959505}, issn = {2076-0817}, support = {Ricerca Corrente 2020 and 2021//Italian Ministry of Health/ ; }, abstract = {A growing body of evidence shows that dysbiotic gut microbiota may correlate with a wide range of disorders; hence, the clinical use of microbiota maps and fecal microbiota transplantation (FMT) can be exploited in the clinic of some infectious diseases. Through direct or indirect ecological and functional competition, FMT may stimulate decolonization of pathogens or opportunistic pathogens, modulating immune response and colonic inflammation, and restoring intestinal homeostasis, which reduces host damage. Herein, we discuss how diagnostic parasitology may contribute to designing clinical metagenomic pipelines and FMT programs, especially in pediatric subjects. The consequences of more specialized diagnostics in the context of gut microbiota communities may improve the clinical parasitology and extend its applications to the prevention and treatment of several communicable and even noncommunicable disorders.}, }
@article {pmid34620937, year = {2021}, author = {Ijoma, GN and Nkuna, R and Mutungwazi, A and Rashama, C and Matambo, TS}, title = {Applying PICRUSt and 16S rRNA functional characterisation to predicting co-digestion strategies of various animal manures for biogas production.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19913}, pmid = {34620937}, issn = {2045-2322}, mesh = {*Anaerobiosis ; Animal Feed ; Animals ; Bacteria/classification/genetics ; *Biofuels ; Computational Biology/methods ; *Fermentation ; Manure/*microbiology ; Metagenome ; Metagenomics/*methods ; Methane/biosynthesis ; Phylogeny ; *RNA, Ribosomal, 16S ; }, abstract = {An estimated 25 million tons of animal manure is produced globally every year, causing considerable impact to the environment. These impacts can be managed through the use of anaerobic digestion (AD) This process achieves waste degradation through enzymatic activity, the efficiency of the AD process is directly related to microorganisms that produce these enzymes. Biomethane potential (BMP) assays remain the standard theoretical framework to pre-determine biogas yield and have been used to determine the feasibility of substrates or their combination for biogas production. However, an integrated approach that combines substrate choice and co-digestion would provide an improvement to the current predictive models. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) addresses the limitations of assays in this regard. In this paper, the biochemical functions of horse, cow, and pig manures are predicted. A total of 135 predicted KEGG Orthologies (KOs) showed amino acids, carbohydrate, energy, lipid, and xenobiotic metabolisms in all the samples. Linear discriminant analysis (LDA) combined with the effect size measurements (LEfSe), showed that fructose, mannose, amino acid and nucleotide sugar, phosphotransferase (PST) as well as starch and sucrose metabolisms were significantly higher in horse manure samples. 36 of the KOs were related to the acidogenesis and/or acetogenesis AD stages. Extended bar plots showed that 11 significant predictions were observed for horse-cow, while 5 were predicted for horse-pig and for cow-pig manures. Based on these predictions, the AD process can be enhanced through co-digestion strategies that takes into account the predicted metabolic contributions of the manure samples. The results supported the BMP calculations for the samples in this study. Biogas yields can be improved if this combined approach is employed in routine analysis before co-digesting different substrates.}, }
@article {pmid34613762, year = {2021}, author = {Wagner, E and Fagerlund, A and Langsrud, S and Møretrø, T and Jensen, MR and Moen, B}, title = {Surveillance of Listeria monocytogenes: Early Detection, Population Dynamics, and Quasimetagenomic Sequencing during Selective Enrichment.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {24}, pages = {e0177421}, pmid = {34613762}, issn = {1098-5336}, support = {294910//Norges Forskningsråd (Forskningsrådet)/ ; 314743//Foundation for Research Levy on Agricultural Products (FFL)/ ; }, mesh = {*Food Microbiology ; Genes, Bacterial ; *Listeria monocytogenes/genetics/isolation &amp; purification ; Metagenomics ; *Microbiota ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, we addressed different aspects regarding the implementation of quasimetagenomic sequencing as a hybrid surveillance method in combination with enrichment for early detection of Listeria monocytogenes in the food industry. Different experimental enrichment cultures were used, comprising seven L. monocytogenes strains of different sequence types (STs), with and without a background microbiota community. To assess whether the proportions of the different STs changed over time during enrichment, the growth and population dynamics were assessed using dapE colony sequencing and dapE and 16S rRNA amplicon sequencing. There was a tendency of some STs to have a higher relative abundance during the late stage of enrichment when L. monocytogenes was enriched without background microbiota. When coenriched with background microbiota, the population dynamics of the different STs was more consistent over time. To evaluate the earliest possible time point during enrichment that allows the detection of L. monocytogenes and at the same time the generation of genetic information that enables an estimation regarding the strain diversity in a sample, quasimetagenomic sequencing was performed early during enrichment in the presence of the background microbiota using Oxford Nanopore Technologies Flongle and Illumina MiSeq sequencing. The application of multiple displacement amplification (MDA) enabled detection of L. monocytogenes (and the background microbiota) after only 4 h of enrichment using both applied sequencing approaches. The MiSeq sequencing data additionally enabled the prediction of cooccurring L. monocytogenes strains in the samples. IMPORTANCE We showed that a combination of a short primary enrichment combined with MDA and Nanopore sequencing can accelerate the traditional process of cultivation and identification of L. monocytogenes. The use of Illumina MiSeq sequencing additionally allowed us to predict the presence of cooccurring L. monocytogenes strains. Our results suggest quasimetagenomic sequencing is a valuable and promising hybrid surveillance tool for the food industry that enables faster identification of L. monocytogenes during early enrichment. Routine application of this approach could lead to more efficient and proactive actions in the food industry that prevent contamination and subsequent product recalls and food destruction, economic and reputational losses, and human listeriosis cases.}, }
@article {pmid33580146, year = {2021}, author = {Brown, CL and Keenum, IM and Dai, D and Zhang, L and Vikesland, PJ and Pruden, A}, title = {Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3753}, pmid = {33580146}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/pharmacology ; Computational Biology/methods ; Drug Resistance, Microbial/*genetics ; Environmental Microbiology ; Environmental Monitoring/methods ; Genome, Bacterial/drug effects ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/drug effects/*genetics ; Metagenomics/methods ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; Waste Water/*analysis ; }, abstract = {In the fight to limit the global spread of antibiotic resistance, the assembly of environmental metagenomes has the potential to provide rich contextual information (e.g., taxonomic hosts, carriage on mobile genetic elements) about antibiotic resistance genes (ARG) in the environment. However, computational challenges associated with assembly can impact the accuracy of downstream analyses. This work critically evaluates the impact of assembly leveraging short reads, nanopore MinION long-reads, and a combination of the two (hybrid) on ARG contextualization for ten environmental metagenomes using seven prominent assemblers (IDBA-UD, MEGAHIT, Canu, Flye, Opera-MS, metaSpades and HybridSpades). While short-read and hybrid assemblies produced similar patterns of ARG contextualization, raw or assembled long nanopore reads produced distinct patterns. Based on an in-silico spike-in experiment using real and simulated reads, we show that low to intermediate coverage species are more likely to be incorporated into chimeric contigs across all assemblers and sequencing technologies, while more abundant species produce assemblies with a greater frequency of inversions and insertion/deletions (indels). In sum, our analyses support hybrid assembly as a valuable technique for boosting the reliability and accuracy of assembly-based analyses of ARGs and neighboring genes at environmentally-relevant coverages, provided that sufficient short-read sequencing depth is achieved.}, }
@article {pmid34959064, year = {2021}, author = {Zhuang, JL and Sun, X and Zhao, WQ and Zhang, X and Zhou, JJ and Ni, BJ and Liu, YD and Shapleigh, JP and Li, W}, title = {The anammox coupled partial-denitrification process in an integrated granular sludge and fixed-biofilm reactor developed for mainstream wastewater treatment: Performance and community structure.}, journal = {Water research}, volume = {210}, number = {}, pages = {117964}, doi = {10.1016/j.watres.2021.117964}, pmid = {34959064}, issn = {1879-2448}, abstract = {This study describes an integrated granular sludge and fixed-biofilm (iGB) reactor innovatively designed to carry out the anammox/partial-denitrification (A/PD) process for nitrogen removal with mainstream municipal wastewater. The iGB-A/PD reactor consists of anammox granules inoculated in the lower region of reactor and an acclimated fixed-biofilm positioned in the upper region. Compared to the other reported A/PD systems for mainstream wastewater treatment, this iGB-A/PD reactor is notable due to its higher quality effluent with a total inorganic nitrogen (TIN) of ∼3 mg•L-1 and operation at a high nitrogen removal rate (NRR) of 0.8 ± 0.1 kg-N•m-3•d-1. Reads-based metatranscriptomic analysis found that the expression values of hzsA and hdh, key genes associated with anammox, were much higher than other functional genes on nitrogen conversion, confirming the major roles of the anammox bacteria in nitrogen bio-removal. In both regions of the reactor, the nitrate reduction genes (napA/narG) had expression values of 56-99 RPM, which were similar to that of the nitrite reduction genes (nirS/nirK). The expression reads from genes for dissimilatory nitrate reduction to ammonium (DNRA), nrfA and nirB, were unexpectedly high, and were over the half of the levels of reads from genes required for nitrate reduction. Kinetic assays confirmed that the granules had an anammox activity of 16.2 g-NH4+-N•kg-1-VSS•d-1 and a nitrate reduction activity of 4.1 g-N•kg-1-VSS•d-1. While these values were changed to be 4.9 g- NH4+-N•kg-1-VSS•d-1and 4.3 g-N•kg-1-VSS•d-1 respectively in the fixed-biofilm. Mass flux determination found that PD and DNRA was responsible for ∼50% and ∼25% of nitrate reduction, respectively, in the whole reactor, consistent with high effluent quality and treatment efficiency via a nitrite loop. Metagenomic binning analysis revealed that new and unidentified anammox species, affiliated with Candidatus Brocadia, were the dominant anammox organisms. Myxococcota and Planctomycetota were the principal organisms associated with the PD and DNRA processes, respectively.}, }
@article {pmid34957455, year = {2021}, author = {Mun, D and Kim, H and Shin, M and Ryu, S and Song, M and Oh, S and Kim, Y}, title = {Decoding the intestinal microbiota repertoire of sow and weaned pigs using culturomic and metagenomic approaches.}, journal = {Journal of animal science and technology}, volume = {63}, number = {6}, pages = {1423-1432}, doi = {10.5187/jast.2021.e124}, pmid = {34957455}, issn = {2055-0391}, abstract = {To elucidate the role and mechanism of microbes, we combined culture-dependent and culture-independent approaches to investigate differences in gut bacterial composition between sows and weaned pigs. Under anaerobic conditions, several nonselective and selective media were used for isolation from fecal samples. All isolated bacteria were identified and classified through 16S rRNA sequencing, and the microbiota composition of the fecal samples was analyzed by metagenomics using next generation sequencing (NGS) technology. A total of 278 and 149 colonies were acquired from the sow and weaned pig fecal samples, respectively. Culturomics analysis revealed that diverse bacterial genus and species belonged to Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were isolated from sow and weaned pigs. When comparing culture-dependent and culture-independent analyses, 191 bacterial species and 2 archaeal bacterial species were detected through culture-independent analysis, and a total of 23 bacteria were isolated through a culture-dependent approach, of which 65% were not detected by metagenomics. In conclusion, culturomics and metagenomics should be properly combined to fully understand the intestinal microbiota, and livestock-derived microbial resources should be informed by culturomic approaches to understand and utilize the mechanism of host-microbe interactions.}, }
@article {pmid34956932, year = {2021}, author = {Li, Z and Chen, G and Wang, P and Sun, M and Zhao, J and Li, A and Sun, Q}, title = {Alterations of the Oral Microbiota Profiles in Chinese Patient With Oral Cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {780067}, doi = {10.3389/fcimb.2021.780067}, pmid = {34956932}, issn = {2235-2988}, abstract = {Oral cancer is the most common malignant tumor in the oral and maxillofacial region, of which more than 90% is squamous cell carcinoma. The incidence of oral cancer is on the rise worldwide. An imbalance between the microorganism composition and its host may lead to the occurrence of oral malignant tumors. Accumulating evidence suggests that the oral microbiota plays an important role in oral cancer; however, the association between oral microbiota and oral cancer has not yet been comprehensively studied. In this study, metagenomic sequencing was used to compare the microbial composition of three groups of samples from Chinese patients with oral cancer, patients with precancerous lesion, and normal individuals. In terms of microbiota richness, the oral microbiota of patients with precancerous lesions was richer than that of oral cancer patients and healthy controls, whereas in terms of microbiota diversity, there was little difference between the three groups. The three groups of samples exhibited statistically significant differences in microbiota composition and metabolic function at the family, genus, and species levels (P < 0.05). The differentially enriched phylum in oral cancer samples was Bacteroidetes (P < 0.05). At the genus level, the main differentially enriched taxa were Prevotella, Peptostreptococcus, Carnobacterium, and Diastella (P < 0.05). The species level was differentially enriched in Prevotella intermedia and Peptostreptococcus stomatis (p < 0.05). The prediction of microbiota function shows that oral cancer is mainly associated with coenzyme A biosynthesis, phosphopantothenic acid biosynthesis, inosine 5'-phosphate degradation, and riboflavin biosynthesis. Furthermore, the increase in C-reactive protein level in oral cancer patients was found to be closely related to P. intermedia. Overall, oral bacterial profiles showed significant differences between the oral cancer group and normal group. Hence, microbes can be employed as diagnostic markers and treatment targets for oral cancer.}, }
@article {pmid34956162, year = {2021}, author = {Xie, Y and Sun, J and Hu, C and Ruan, B and Zhu, B}, title = {Oral Microbiota Is Associated With Immune Recovery in Human Immunodeficiency Virus-Infected Individuals.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {794746}, doi = {10.3389/fmicb.2021.794746}, pmid = {34956162}, issn = {1664-302X}, abstract = {The role of the oral microbiota in HIV-infected individuals deserves attention as either HIV infection or antiretroviral therapy (ART) may have effect on the diversity and the composition of the oral microbiome. However, few studies have addressed the oral microbiota and its interplay with different immune responses to ART in HIV-infected individuals. Salivary microbiota and immune activation were studied in 30 HIV-infected immunological responders (IR) and 34 immunological non-responders (INR) (≥500 and < 200 CD4 + T-cell counts/μl after 2 years of HIV-1 viral suppression, respectively) with no comorbidities. Metagenome sequencing revealed that the IR and the INR group presented similar salivary bacterial richness and diversity. The INR group presented a significantly higher abundance of genus Selenomonas_4, while the IR group manifested higher abundances of Candidatus_Saccharimonas and norank_p_Saccharimonas. Candidatus_Saccharimonas and norank_p_Saccharimonas were positively correlated with the current CD4 + T-cells. Candidatus_Saccharimonas was positively correlated with the markers of adaptive immunity CD4 + CD57 + T-cells, while negative correlation was found between norank _p_Saccharimonas and the CD8 + CD38 + T-cells as well as the CD4/CD8 + HLADR + CD38 + T-cells. The conclusions are that the overall salivary microbiota structure was similar in the immunological responders and immunological non-responders, while there were some taxonomic differences in the salivary bacterial composition. Selenomona_4, Candidatus_Saccharimonas, and norank _p_Saccharimonas might act as important factors of the immune recovery in the immunodeficiency patients, and Candidatus_Saccharimonas could be considered in the future as screening biomarkers for the immune responses in the HIV-infected individuals.}, }
@article {pmid34956130, year = {2021}, author = {Corrêa, PS and Jimenez, CR and Mendes, LW and Rymer, C and Ray, P and Gerdes, L and da Silva, VO and De Nadai Fernandes, EA and Abdalla, AL and Louvandini, H}, title = {Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {768480}, doi = {10.3389/fmicb.2021.768480}, pmid = {34956130}, issn = {1664-302X}, abstract = {The importance of beef production for economy of Brazil and the growing demand for animal protein across the globe warrant an improvement in the beef production system. Although most attention has been on modulation of the rumen microbiome to improve ruminant production, the role of the lower gut microbiome in host health and nutrition remains relatively unexplored. This work aimed to investigate the taxonomy and functional variations in the fecal microbiome of Brazilian beef cattle reared in two different production systems using a metagenomic approach. Sixty male beef cattle from six farms representing semi-intensive (I, n = 2) and traditional (T, n = 4) Brazilian beef production systems were enrolled in the study. Shotgun sequencing was used to characterize taxonomic and functional composition and diversity of the microbiome in fecal samples collected from each animal. Fecal samples were analyzed for copper (Cu), lead (Pb), nitrogen (N), phosphorous (P), selenium (Se), and zinc (Zn) and stable isotopes of carbon (13C) and nitrogen (15N). The fecal microbiome was influenced by the beef production systems with greater functional and lower taxonomic diversity in beef cattle feces from I systems compared with that from T systems. The concentration of N, P, and Zn was higher in beef cattle feces from I systems compared with that from T systems and was associated with taxonomic and functional profile of fecal microbiome in I system, suggesting the role of fecal nutrients in shaping system-specific microbiome. Semi-intensive management practices led to a more complex but less connected fecal microbiome in beef cattle. The microbial community in beef cattle feces from I systems was characterized by greater abundance of beneficial bacteria (phylum Firmicutes and butyrate-producing bacteria family Lachnospiraceae and genera Anaerostipes, Blautia, Butyrivibrio, Eubacterium, Roseburia, and Ruminococcus). In addition, the fecal abundance of microbial genes related to immune system, nutrient metabolism, and energy production was greater in beef cattle raised under I systems compared with that under T systems. Findings of the current study suggest that semi-intensive management practices could facilitate the development of a healthier and more efficient fecal microbiome in beef cattle by driving an increase in the abundance of beneficial bacteria and functional genes.}, }
@article {pmid34956127, year = {2021}, author = {Blumberg, KL and Ponsero, AJ and Bomhoff, M and Wood-Charlson, EM and DeLong, EF and Hurwitz, BL}, title = {Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {765268}, doi = {10.3389/fmicb.2021.765268}, pmid = {34956127}, issn = {1664-302X}, abstract = {Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven't been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making 'omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended.}, }
@article {pmid34956112, year = {2021}, author = {Teng, JLL and Wernery, U and Lee, HH and Fung, J and Joseph, S and Li, KSM and Elizabeth, SK and Fong, JYH and Chan, KH and Chen, H and Lau, SKP and Woo, PCY}, title = {Co-circulation of a Novel Dromedary Camel Parainfluenza Virus 3 and Middle East Respiratory Syndrome Coronavirus in a Dromedary Herd With Respiratory Tract Infections.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {739779}, doi = {10.3389/fmicb.2021.739779}, pmid = {34956112}, issn = {1664-302X}, abstract = {Since the emergence of Middle East Respiratory Syndrome (MERS) in 2012, there have been a surge in the discovery and evolutionary studies of viruses in dromedaries. Here, we investigated a herd of nine dromedary calves from Umm Al Quwain, the United Arab Emirates that developed respiratory signs. Viral culture of the nasal swabs from the nine calves on Vero cells showed two different types of cytopathic effects (CPEs), suggesting the presence of two different viruses. Three samples showed typical CPEs of Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) in Vero cells, which was confirmed by partial RdRp gene sequencing. Complete genome sequencing of the three MERS-CoV strains showed that they belonged to clade B3, most closely related to another dromedary MERS-CoV isolate previously detected in Dubai. They also showed evidence of recombination between lineages B4 and B5 in ORF1ab. Another three samples showed non-typical CPEs of MERS-CoV with cell rounding, progressive degeneration, and detachment. Electron microscopy revealed spherical viral particles with peplomers and diameter of about 170nm. High-throughput sequencing and metagenomic analysis showed that the genome organization (3'-N-P-M-F-HN-L-5') was typical of paramyxovirus. They possessed typical genome features similar to other viruses of the genus Respirovirus, including a conserved motif 323FAPGNYALSYAM336 in the N protein, RNA editing sites 5'-717AAAAAAGGG725-3', and 5'-1038AGAAGAAAGAAAGG1051-3' (mRNA sense) in the P gene with multiple polypeptides coding capacity, a nuclear localization signal sequence 245KVGRMYSVEYCKQKIEK261 in the M protein, a conserved sialic acid binding motif 252NRKSCS257 in the HN protein, conserved lengths of the leader (55nt) and trailer (51nt) sequences, total coding percentages (92.6-93.4%), gene-start (AGGANNAAAG), gene-end (NANNANNAAAAA), and trinucleotide intergenic sequences (CTT, mRNA sense). Phylogenetic analysis of their complete genomes showed that they were most closely related to bovine parainfluenza virus 3 (PIV3) genotype C strains. In the phylogenetic tree constructed using the complete L protein, the branch length between dromedary camel PIV3 (DcPIV3) and the nearest node is 0.04, which is >0.03, the definition used for species demarcation in the family Paramyxoviridae. Therefore, we show that DcPIV3 is a novel species of the genus Respirovirus that co-circulated with MERS-CoV in a dromedary herd in the Middle East.}, }
@article {pmid34955122, year = {2021}, author = {Zheng, R and Zhang, Y and Rong, Z and Huang, W and Fu, X}, title = {[Surviving Sepsis Campaign: international guidelines for management of sepsis and septic shock 2021, interpretation and expectation].}, journal = {Zhonghua wei zhong bing ji jiu yi xue}, volume = {33}, number = {10}, pages = {1159-1164}, doi = {10.3760/cma.j.cn121430-20211009-01442}, pmid = {34955122}, issn = {2095-4352}, abstract = {The Surviving Sepsis Campaign: international guidelines for management of sepsis and septic shock 2021 (2021 guidelines) was recently released. The guidelines summarized the evidences from literatures up to July 2019, and composed by 6 parts as "screening and early treatment", "infection", "hemodynamic management", "ventilation", "additional therapies" and "long-term outcomes and goals of care" with a total of 93 items and 99 recommendations. Compared with the 2016 guidelines (96 recommendations), although the total number of recommendations in the 2021 guidelines is similar, the number of "strong recommendations (recommend)" in 2021 guidelines has dropped significantly, as the number of "weak recommendations (suggest)" has increased significantly, and the level of the quality of evidence on which the recommendations are based has been significantly lowered. Furthermore, 2021 guidelines have also markedly deleted or simplified the recommendations regarding infection prevention, acute respiratory distress syndrome (ARDS) treatment, nutritional support and so on. While, the most obvious improvement appears in the segment of "long-term outcomes and goals of care", in which the patients and their families could get help in term of determining their physical rehabilitation and discharge follow-up plans and formulating exact goals of care. 2021 guidelines did not adopt new and emerging therapies or treatments, such as metagenomic next-generation sequencing (mNGS), diaphragm protective ventilation, timing of initiating renal replacement therapy for acute kidney injury, early mobility, endotoxin adsorption, tranexamic acid, E-medicine and telemedicine, big data and artificial intelligence and other new therapies. Collectively, it may suggest the 2021 guidelines tend to be conservative and simplified rather than fairly optimized and logicalized, which may arouse controversy in the future and affect clinician compliance.}, }
@article {pmid34954826, year = {2021}, author = {Speruda, M and Piecuch, A and Borzęcka, J and Kadej, M and Ogórek, R}, title = {Microbial traces and their role in forensic science.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15426}, pmid = {34954826}, issn = {1365-2672}, abstract = {Forensic microbiology, also known as the microbiology of death, is an emerging branch of science that is still underused in criminal investigations. Some of the cases might be difficult to solve with commonly-used forensic methods, and then they become an operational field for microbiological and mycological analysis. The aim of our review is to present significant achievements of selected studies on the thanatomicrobiome (microorganisms found in the body, organs and fluids after death) and epinecrotic community (microorganisms found on decaying corpses) that can be used in forensic sciences. Research carried out as a part of the forensic microbiology deals with the thanatomicrobiome and the necrobiome - communities of microorganisms that live inside and outside of a putrefying corpse. Change of species composition observed in each community is a valuable feature that gives a lot of information related to the crime. It is mainly used in the estimation of post-mortem interval (PMI). In some criminal investigations, such noticeable changes in the microbiome and mycobiome can determine the cause or the actual place of death. The microbial traces found at the crime scene can also provide clear evidence of guilt. Nowadays, identification of microorganisms isolated from the body or environment is based on metagenome analysis and 16S rRNA gene amplicon-based sequencing for bacteria and ITS rRNA gene amplicon-based sequencing for fungi. Cultivation methods are still in use and seem to be more accurate; however, they require much more time to achieve a final result, which is an unwanted feature in any criminal investigation.}, }
@article {pmid34954661, year = {2021}, author = {Van Brussel, K and Holmes, EC}, title = {Zoonotic disease and virome diversity in bats.}, journal = {Current opinion in virology}, volume = {52}, number = {}, pages = {192-202}, doi = {10.1016/j.coviro.2021.12.008}, pmid = {34954661}, issn = {1879-6265}, abstract = {The emergence of zoonotic viral diseases in humans commonly reflects exposure to mammalian wildlife. Bats (order Chiroptera) are arguably the most important mammalian reservoir for zoonotic viruses, with notable examples including Severe Acute Respiratory Syndrome coronaviruses 1 and 2, Middle East Respiratory Syndrome coronavirus, henipaviruses and lyssaviruses. Herein, we outline our current knowledge on the diversity of bat viromes, particularly through the lens of metagenomic next-generation sequencing and in the context of disease emergence. A key conclusion is that although bats harbour abundant virus diversity, the vast majority of bat viruses have not emerged to cause disease in new hosts such that bats are better regarded as critical but endangered components of global ecosystems.}, }
@article {pmid34954354, year = {2021}, author = {Puig-Castellví, F and Midoux, C and Guenne, A and Conteau, D and Franchi, O and Bureau, C and Madigou, C and Jouan-Rimbaud Bouveresse, D and Kroff, P and Mazéas, L and Rutledge, DN and Gaval, G and Chapleur, O}, title = {Metataxonomics, metagenomics, metabolomics analysis of the influence of temperature modification in full-scale anaerobic digesters.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {126612}, doi = {10.1016/j.biortech.2021.126612}, pmid = {34954354}, issn = {1873-2976}, abstract = {Full-scale anaerobic digesters' performance is regulated by modifying their operational conditions, but little is known about how these modifications affect their microbiome. In this work, we monitored two originally mesophilic (35°C) full-scale anaerobic digesters during 476 days. One digester was submitted to sub-mesophilic (25°C) conditions between days 123 and 373. We characterized the effect of temperature modification using a multi-omics (metataxonomics, metagenomics, and metabolomics) approach. The metataxonomics and metagenomics results revealed that the lower temperature allowed a substantial increase of the sub-dominant bacterial population, destabilizing the microbial community equilibrium and reducing the biogas production. After restoring the initial mesophilic temperature, the bacterial community manifested resilience in terms of microbial structure and functional activity. The metabolomic signature of the sub-mesophilic acclimation was characterized by a rise of amino acids and short peptides, suggesting a protein degradation activity not directed towards biogas production.}, }
@article {pmid34954158, year = {2021}, author = {Zhao, X and Liu, M and Yang, S and Gong, H and Ma, J and Li, C and Wang, K}, title = {Performance and microbial community evaluation of full-scale two-phase anaerobic digestion of waste activated sludge.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152525}, doi = {10.1016/j.scitotenv.2021.152525}, pmid = {34954158}, issn = {1879-1026}, abstract = {"Temperature Staging and Biological Phasing" (TSBP) is an improved two-phase anaerobic digestion (AD) technology. This technology hydrolyzes waste activated sludge (WAS) at 45 °C and converts methane at mesophilic temperature (35-38 °C), with hydraulic retention times of 3-5 d and 14-17 d, respectively. In this study, the performance and microbial community dynamics of full-scale TSBP-based sludge anaerobic digestion system were studied, and the technology was evaluated by energy balance and ecological benefit analysis. The stable operation for 390 d showed that the cumulative biogas yield was about 349,041 m3, the maximum biogas yield rate was 563.68 L/kg VS, and the VS degradation rate of organic matters in the sludge was 47.19%. Proteobacteria and Firmicutes were found to be the dominant bacteria in both thermophilic and mesophilic reactors. Methanobacterium and Methanosarcina were the two most abundant methanogenic genera in the AD samples. The aceticlastic methanogenesis was likely the predominant production pathway of methane in AD processes based on metagenomics. The TSBP system operated stably, and the recovered energy could achieve energy self-sufficiency, which provided technical reference for the anaerobic treatment of sludge.}, }
@article {pmid34954104, year = {2021}, author = {Ai, J and Zhang, H and Yu, S and Li, J and Chen, S and Zhang, W and Mao, R}, title = {A case of fatal amoebic encephalitis caused by Balamuthia mandrillaris, China.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105190}, doi = {10.1016/j.meegid.2021.105190}, pmid = {34954104}, issn = {1567-7257}, abstract = {We reported a case of B.mandrillaris amoebic encephalitis in mainland China. Metagenomics next-generation sequencing helped initial diagnosis and then polymerase chain reaction of the B.mandrillaris in the infected nasal skin tissues reported positive and amoeba cysts were found in the tissue under microscopic observation.}, }
@article {pmid34953835, year = {2021}, author = {Mercado, JV and Koyama, M and Nakasaki, K}, title = {Short-term changes in the anaerobic digestion microbiome and biochemical pathways with changes in organic load.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152585}, doi = {10.1016/j.scitotenv.2021.152585}, pmid = {34953835}, issn = {1879-1026}, abstract = {Fluctuations in organic loading rate are frequently experienced in practical-scale anaerobic digestion systems. These impose shocks to the microbiome leading to process instability and failure. This study elucidated the short-term changes in biochemical pathways and the contributions of microbial groups involved in anaerobic digestion with varying organic load shocks. A mixture of starch and hipolypeptone corresponding to a carbon-to‑nitrogen ratio of 25 was used as substrate. Batch vial reactors were run using acclimatized sludge fed with organic load varying from 0 to 5 g VS/L. Methane yield decreased with increasing organic load. The microbiome alpha diversity represented as the number of operational taxonomic units (OTUs) and the Shannon index both decreased with organic load indicating microbiome specialization. The biochemical pathways predicted using PICRUSt2 were analyzed along with the corresponding contributions of microbial groups leading to a proposed pathway of substrate utilization. Genus Trichococcus (order Lactobacillales) increased in contribution to starch degradation pathways with increase in organic load while genus Macellibacteroides (order Bacteroidales) was prominent in contribution to bacterial anaerobic digestion pathways. Strictly acetoclastic Methanosaeta increased in prominence over hydrogenotrophic Methanolinea with increase in organic load. Results from this study provide better understanding of how anaerobic digesters respond to organic load shocks.}, }
@article {pmid34952941, year = {2021}, author = {Saheb Kashaf, S and Proctor, DM and Deming, C and Saary, P and Hölzer, M and ,  and Taylor, ME and Kong, HH and Segre, JA and Almeida, A and Finn, RD}, title = {Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {34952941}, issn = {2058-5276}, abstract = {Human skin functions as a physical barrier to foreign pathogen invasion and houses numerous commensals. Shifts in the human skin microbiome have been associated with conditions ranging from acne to atopic dermatitis. Previous metagenomic investigations into the role of the skin microbiome in health or disease have found that much of the sequenced data do not match reference genomes, making it difficult to interpret metagenomic datasets. We combined bacterial cultivation and metagenomic sequencing to assemble the Skin Microbial Genome Collection (SMGC), which comprises 622 prokaryotic species derived from 7,535 metagenome-assembled genomes and 251 isolate genomes. The metagenomic datasets that we generated were combined with publicly available skin metagenomic datasets to identify members and functions of the human skin microbiome. The SMGC collection includes 174 newly identified bacterial species and 12 newly identified bacterial genera, including the abundant genus 'Candidatus Pellibacterium', which has been newly associated with the skin. The SMGC increases the characterized set of known skin bacteria by 26%. We validated the SMGC metagenome-assembled genomes by comparing them with sequenced isolates obtained from the same samples. We also recovered 12 eukaryotic species and assembled thousands of viral sequences, including newly identified clades of jumbo phages. The SMGC enables classification of a median of 85% of skin metagenomic sequences and provides a comprehensive view of skin microbiome diversity, derived primarily from samples obtained in North America.}, }
@article {pmid34952501, year = {2021}, author = {Zhang, Y and Chen, J and Chen, H and Liu, L and Liu, C and Teng, Y}, title = {An integrated multidisciplinary-based framework for characterizing environmental risks of heavy metals and their effects on antibiotic resistomes in agricultural soils.}, journal = {Journal of hazardous materials}, volume = {426}, number = {}, pages = {128113}, doi = {10.1016/j.jhazmat.2021.128113}, pmid = {34952501}, issn = {1873-3336}, abstract = {In this study, a new integrated multidisciplinary-based framework has been proposed to better understand the environmental risks of heavy metals (HMs) in agricultural soils. The source apportionment results revealed by a multilinear engine model were incorporated into the geochemical indexes and the probabilistic health risk assessment models for identifying the source-oriented risks of HMs in the environment. High-throughput sequencing-based metagenomic assembly analysis was used for characterizing the prevalence and dissemination risk of antibiotic resistomes and their associations with the geochemical enrichment of HMs in the soils. Results showed agricultural and industrial activities were the main sources of HMs in the environment. Although the soils were contaminated moderately by HMs and the health risks posed by soil metals were negligible for both adult and children, source-oriented risk evaluation suggested agricultural activities contributed relatively higher contamination and health risks than the other sources. Notably, abundant and diverse antibiotic resistant genes, mobile gene elements, virulence factors, and antibiotic-resistant bacterial pathogens were identified in the agricultural soils, as well as their co-occurrences on the same contigs, implying a non-negligible resistome risk. Further, statistical and network analyses showed the geochemical enrichment of HMs exerted significant effects on the antibiotic resistomes in the environment.}, }
@article {pmid34952209, year = {2021}, author = {Conchouso, D and Al-Ma'abadi, A and Behzad, H and Alarawi, M and Hosokawa, M and Nishikawa, Y and Takeyama, H and Mineta, K and Gojobori, T}, title = {Integration of Droplet Microfluidic Tools for Single-cell Functional Metagenomics: An Engineering Head Start.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.gpb.2021.03.010}, pmid = {34952209}, issn = {2210-3244}, abstract = {Droplet microfluidic techniques have shown promising results to study single cells at high throughput. However, their adoption in laboratories studying "-omics" sciences is still irrelevant because of the field's complex and multidisciplinary nature. To facilitate their use, here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput. First, a device encapsulating single cells in droplets at a rate of ∼ 250 Hz is described considering droplet size and cell growth. Then, we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers (i.e., 405, 488, 561, and 637 nm) in a single platform to make it compatible with different fluorescence-emitting biosensors. For this sorter, both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz. Then, a passive droplet merger is also integrated into our method to enable adding new reagents to already-made droplets at a rate of 200 Hz. Finally, we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools. Because of the overall integration and the technical details presented here, our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability (> 50,000 cells/day) to mining and bioprospecting metagenomic data.}, }
@article {pmid34951686, year = {2021}, author = {Trivedi, K and Kumar, R and Vijay Anand, KG and Bhojani, G and Kubavat, D and Ghosh, A}, title = {Structural and functional changes in soil bacterial communities by drifting spray application of a commercial red seaweed extract as revealed by metagenomics.}, journal = {Archives of microbiology}, volume = {204}, number = {1}, pages = {72}, pmid = {34951686}, issn = {1432-072X}, support = {MLP 0016//council of scientific and industrial research, india/ ; }, abstract = {Kappaphycus alvarezii seaweed extract (KSWE) is known to enhance crop productivity and impart stress tolerance. Close to one quarter of foliar spray applied to maize falls on the soil, either as drift or from leaf as drip. It was hypothesized that the drift spray would profoundly influence soil microbes under stress. An experiment was conducted with five treatments, with or without KSWE application at critical stages of maize grown under soil moisture stress and compared with an irrigated control. An Illumina platform was employed for the analysis of the V3-V4 region of 16S rRNA gene from the soil metagenome. A total of 345,552 operational taxonomic units were generated which were classified into 55 phyla, 152 classes, 240 orders, 305 families and 593 genera. Shannon's index and Shannon's equitability indicated increased soil bacterial diversity after multiple KSWE applications under conditions of abiotic duress. The abundance of the genera Alicyclobacillus, Anaerolinea, Bacillus, Balneimonas, Nitrospira, Rubrobacter and Steroidobacter decreased (49-79%) under drought imposed at the V5,10 and 15 stages of maize over the irrigated control, while it significantly improved when followed by KSWE application under drought. Flavobacterium, Nitrosomonas, Nitrosovibrio, Rubrobacter genera and several other bacterial taxa which are important for plant growth promotion and nutrient cycling were found to be enriched by KSWE application under drought conditions. Treatments having enriched microbial abundance due to KSWE application under stress recorded higher soil enzymatic activities and plant cob yield, suggesting the contribution of altered soil ecology mediated by KSWE as one of the reasons for improvement of yield.}, }
@article {pmid34951470, year = {2021}, author = {Graff, K and Dominguez, SR and Messacar, K}, title = {Metagenomic Next-Generation Sequencing for Diagnosis of Pediatric Meningitis and Encephalitis: A Review.}, journal = {Journal of the Pediatric Infectious Diseases Society}, volume = {10}, number = {Supplement_4}, pages = {S78-S87}, doi = {10.1093/jpids/piab067}, pmid = {34951470}, issn = {2048-7207}, support = {K23AI28069//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Child ; *Encephalitis/diagnosis ; High-Throughput Nucleotide Sequencing ; Humans ; *Meningitis/diagnosis ; Metagenomics ; *Viruses ; }, abstract = {Metagenomic next-generation sequencing is a novel diagnostic test with the potential to revolutionize the diagnosis of pediatric meningitis and encephalitis through unbiased detection of bacteria, viruses, parasites, and fungi in cerebrospinal fluid. Current literature is mostly observational with variable indications, populations, and timing of testing with resulting variability in diagnostic yield and clinical impact. Diagnostic stewardship strategies are needed to direct testing toward high-impact pediatric populations, to optimize timing of testing, to ensure appropriate interpretation of results, and to guide prompt optimization of antimicrobials. This review highlights the high clinical potential of this test, though future studies are needed to gather clinical impact and cost-effectiveness data for specific indications in pediatric populations.}, }
@article {pmid34951468, year = {2021}, author = {Handel, AS and Muller, WJ and Planet, PJ}, title = {Metagenomic Next-Generation Sequencing (mNGS): SARS-CoV-2 as an Example of the Technology's Potential Pediatric Infectious Disease Applications.}, journal = {Journal of the Pediatric Infectious Diseases Society}, volume = {10}, number = {Supplement_4}, pages = {S69-S70}, doi = {10.1093/jpids/piab108}, pmid = {34951468}, issn = {2048-7207}, mesh = {*COVID-19 ; Child ; *Communicable Diseases ; High-Throughput Nucleotide Sequencing ; Humans ; SARS-CoV-2 ; Sensitivity and Specificity ; Technology ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has emerged as a potentially powerful tool in clinical diagnosis, hospital epidemiology, microbial evolutionary biology, and studies of host-pathogen interaction. The SARS-CoV-2 pandemic provides a framework for demonstrating the applications of this technology in each of these areas. In this Supplement, we review applications of mNGS within the discipline of pediatric infectious diseases.}, }
@article {pmid34951467, year = {2021}, author = {Haslam, DB}, title = {Future Applications of Metagenomic Next-Generation Sequencing for Infectious Diseases Diagnostics.}, journal = {Journal of the Pediatric Infectious Diseases Society}, volume = {10}, number = {Supplement_4}, pages = {S112-S117}, doi = {10.1093/jpids/piab107}, pmid = {34951467}, issn = {2048-7207}, mesh = {*Communicable Diseases/diagnosis ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Sensitivity and Specificity ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has the theoretical capacity to detect any microbe present in a host. mNGS also has the potential to infer a pathogen's phenotypic characteristics, including the ability to colonize humans, cause disease, and resist treatment. Concurrent host nucleic acid sequencing can assess the infected individual's physiological state, including characterization and appropriateness of the immune response. When the pathogen cannot be identified, host RNA sequencing may help infer the organism's nature. While the full promise of mNGS remains far from realization, the potential ability to identify all microbes in a complex clinical sample, assess each organism's virulence and antibiotic susceptibility traits, and simultaneously characterize the host's response to infection provide opportunities for mNGS to supplant existing technologies and become the primary method of infectious diseases diagnostics.}, }
@article {pmid34951466, year = {2021}, author = {Edward, P and Handel, AS}, title = {Metagenomic Next-Generation Sequencing for Infectious Disease Diagnosis: A Review of the Literature With a Focus on Pediatrics.}, journal = {Journal of the Pediatric Infectious Diseases Society}, volume = {10}, number = {Supplement_4}, pages = {S71-S77}, doi = {10.1093/jpids/piab104}, pmid = {34951466}, issn = {2048-7207}, mesh = {Child ; *Communicable Diseases/diagnosis ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Pediatrics ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is a novel tool for identifying microbial DNA and/or RNA in blood and other clinical specimens. In the face of increasingly complex patients and an ever-growing list of known potential pathogens, mNGS has been proposed as a breakthrough tool for unbiased pathogen identification. Studies have begun to explore the clinical applicability of mNGS in a variety of settings, including endocarditis, pneumonia, febrile neutropenia, osteoarticular infections, and returning travelers. The real-world impact of mNGS has also been assessed through retrospective studies, documenting varying degrees of success and limitations. In this review, we will explore current highlights of the clinical mNGS literature, with a focus on pediatric data where available. We aim to provide the reader with a deeper understanding of the strengths and weaknesses of mNGS and to provide direction toward areas requiring further research.}, }
@article {pmid34951405, year = {2021}, author = {Buysse, M and Floriano, AM and Gottlieb, Y and Nardi, T and Comandatore, F and Olivieri, E and Giannetto, A and Palomar, AM and Makepeace, BL and Bazzocchi, C and Cafiso, A and Sassera, D and Duron, O}, title = {A dual endosymbiosis supports nutritional adaptation to hematophagy in the invasive tick Hyalomma marginatum.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, doi = {10.7554/eLife.72747}, pmid = {34951405}, issn = {2050-084X}, support = {EVOSYM//Ministry of Science, Technology and Space/ ; EVOSYM//Centre National de la Recherche Scientifique/ ; 1074/18//Israel Science Foundation/ ; RGY0075/2017//Human Frontier Science Program/ ; ANR-21-CE02-0002//Centre National de la Recherche Scientifique/ ; }, abstract = {Many animals are dependent on microbial partners that provide essential nutrients lacking from their diet. Ticks, whose diet consists exclusively on vertebrate blood, rely on maternally inherited bacterial symbionts to supply B vitamins. While previously studied tick species consistently harbor a single lineage of those nutritional symbionts, we evidence here that the invasive tick Hyalomma marginatum harbors a unique dual-partner nutritional system between an ancestral symbiont, Francisella, and a more recently acquired symbiont, Midichloria. Using metagenomics, we show that Francisella exhibits extensive genome erosion that endangers the nutritional symbiotic interactions. Its genome includes folate and riboflavin biosynthesis pathways but deprived functional biotin biosynthesis on account of massive pseudogenization. Co-symbiosis compensates this deficiency since the Midichloria genome encompasses an intact biotin operon, which was primarily acquired via lateral gene transfer from unrelated intracellular bacteria commonly infecting arthropods. Thus, in H. marginatum, a mosaic of co-evolved symbionts incorporating gene combinations of distant phylogenetic origins emerged to prevent the collapse of an ancestral nutritional symbiosis. Such dual endosymbiosis was never reported in other blood feeders but was recently documented in agricultural pests feeding on plant sap, suggesting that it may be a key mechanism for advanced adaptation of arthropods to specialized diets.}, }
@article {pmid34951085, year = {2021}, author = {Chen, L and Li, L and Zhang, S and Zhang, W and Xue, K and Wang, Y and Dong, X}, title = {Anaerobic methane oxidation linked to Fe(III) reduction in a Candidatus Methanoperedens-enriched consortium from the cold Zoige wetland at Tibetan Plateau.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15848}, pmid = {34951085}, issn = {1462-2920}, support = {32070061//National Natural Science Foundation of China/ ; 91751203//National Natural Science Foundation of China/ ; }, abstract = {Anaerobic oxidation of methane (AOM) is a microbial process degrading ample methane in anoxic environments, and Ca. Methanoperedens mediated nitrate- or metal-reduction linked AOM is believed important in freshwater systems. This work, via 16S rRNA gene diversity survey and 16S rRNA quantification, found abundant Ca. Methanoperedens along with iron in the cold Zoige wetland at Tibetan Plateau. The wetland soil microcosm performed Fe(III) reduction, rather than nitrate- nor sulphate-reduction, coupled methane oxidation (3.87 μmol d-1) with 32.33 μmol Fe(II) accumulation per day at 18°C, but not at 30°C. A metagenome-assembled genome (MAG) recovered from the microcosm exhibits ~74% average nucleotide identity with the reported Ca. Methanoperedens spp. that perform Fe(III) reduction linked AOM, thus a novel species Ca. Methanoperedens psychrophilus was proposed. Ca. M. psychrophilus contains the whole suite of CO2 reductive methanogenic genes presumably involving in AOM via a reverse direction, and comparative genome analysis revealed its unique gene categories: the multi-heme clusters (MHCs) cytochromes, the S-layer proteins highly homologous to those recovered from lower temperature environments and type IV pili, those could confer Ca. M. psychrophilus of cold adaptability. Therefore, this work reports the first methanotroph implementing AOM in an alpine wetland.}, }
@article {pmid34950723, year = {2021}, author = {Nessler, JN and Jo, WK and Osterhaus, ADME and Ludlow, M and Tipold, A}, title = {Canine Meningoencephalitis of Unknown Origin-The Search for Infectious Agents in the Cerebrospinal Fluid via Deep Sequencing.}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {645517}, pmid = {34950723}, issn = {2297-1769}, abstract = {Meningoencephalitis of unknown origin (MUO) describes a group of meningoencephalitides in dogs with a hitherto unknown trigger. An infectious agent has been suggested as one possible trigger of MUO but has not been proven so far. A relatively new method to screen for viral RNA or DNA is next-generation sequencing (NGS) or deep sequencing. In this study, a metagenomics analysis of the virome in a sample is analyzed and scanned for known or unknown viruses. We examined fresh-frozen CSF of 6 dogs with MUO via NGS using a modified sequence-independent, single-primer amplification protocol to detect a possible infectious trigger. Analysis of sequencing reads obtained from the six CSF samples showed no evidence of a virus infection. The inability to detect a viral trigger which could be implicated in the development of MUO in the examined population of European dogs, suggests that the current techniques are not sufficiently sensitive to identify a possible virus infection, that the virus is already eliminated at the time-point of disease outbreak, the trigger might be non-infectious or that there is no external trigger responsible for initiating MUO in dogs.}, }
@article {pmid34950118, year = {2021}, author = {Mai, Z and Ye, M and Wang, Y and Foong, SY and Wang, L and Sun, F and Cheng, H}, title = {Characteristics of Microbial Community and Function With the Succession of Mangroves.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {764974}, pmid = {34950118}, issn = {1664-302X}, abstract = {In this study, 16S high-throughput and metagenomic sequencing analyses were employed to explore the changes in microbial community and function with the succession of mangroves (Sonneratia alba, Rhizophora apiculata, and Bruguiera parviflora) along the Merbok river estuary in Malaysia. The sediments of the three mangroves harbored their own unique dominant microbial taxa, whereas R. apiculata exhibited the highest microbial diversity. In general, Gammaproteobacteria, Actinobacteria, Alphaproteobacteria, Deltaproteobacteria, and Anaerolineae were the dominant microbial classes, but their abundances varied significantly among the three mangroves. Principal coordinates and redundancy analyses revealed that the specificity of the microbial community was highly correlated with mangrove populations and environmental factors. The results further showed that R. apiculata exhibited the highest carbon-related metabolism, coinciding with the highest organic carbon and microbial diversity. In addition, specific microbial taxa, such as Desulfobacterales and Rhizobiales, contributed the highest functional activities related to carbon metabolism, prokaryote carbon fixation, and methane metabolism. The present results provide a comprehensive understanding of the adaptations and functions of microbes in relation to environmental transition and mangrove succession in intertidal regions. High microbial diversity and carbon metabolism in R. apiculata might in turn facilitate and maintain the formation of climax mangroves in the middle region of the Merbok river estuary.}, }
@article {pmid34950117, year = {2021}, author = {Wang, X and Wang, Z and Pan, H and Qi, J and Li, D and Zhang, L and Shen, Y and Xiang, Z and Li, M}, title = {Captivity Influences the Gut Microbiome of Rhinopithecus roxellana.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {763022}, pmid = {34950117}, issn = {1664-302X}, abstract = {Ex situ (captivity in zoos) is regarded as an important form of conservation for endangered animals. Many studies have compared differences in the gut microbiome between captive and wild animals, but few have explained those differences at the functional level due to the limited amount of 16S rRNA data. Here, we compared the gut microbiome of captive and wild Rhinopithecus roxellana, whose high degree of dietary specificity makes it a good subject to observe the effects of the captive environment on their gut microbiome, by performing a metagenome-wide association study (MWAS). The Chao1 index was significantly higher in the captive R. roxellana cohort than in the wild cohort, and the Shannon index of captive R. roxellana was higher than that of the wild cohort but the difference was not significant. A significantly increased ratio of Prevotella/Bacteroides, which revealed an increased ability to digest simple carbohydrates, was found in the captive cohort. A significant decrease in the abundance of Firmicutes and enrichment of genes related to the pentose phosphate pathway were noted in the captive cohort, indicating a decreased ability of captive monkeys to digest fiber. Additionally, genes required for glutamate biosynthesis were also significantly more abundant in the captive cohort than in the wild cohort. These changes in the gut microbiome correspond to changes in the composition of the diet in captive animals, which has more simple carbohydrates and less crude fiber and protein than the diet of the wild animals. In addition, more unique bacteria in captive R. roxellana were involved in antibiotic resistance (Acinetobacter) and diarrhea (Desulfovibrio piger), and in the prevention of diarrhea (Phascolarctobacterium succinatutens) caused by Clostridioides difficile. Accordingly, our data reveal the cause-and-effect relationships between changes in the exact dietary composition and changes in the gut microbiome on both the structural and functional levels by comparing of captive and wild R. roxellana.}, }
@article {pmid34949828, year = {2021}, author = {Li, L and Koirala, B and Hernandez, Y and MacIntyre, LW and Ternei, MA and Russo, R and Brady, SF}, title = {Identification of structurally diverse menaquinone-binding antibiotics with in vivo activity against multidrug-resistant pathogens.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {34949828}, issn = {2058-5276}, support = {1U19AI142731//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 5R35GM122559//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; }, abstract = {The emergence of multidrug-resistant bacteria poses a threat to global health and necessitates the development of additional in vivo active antibiotics with diverse modes of action. Directly targeting menaquinone (MK), which plays an important role in bacterial electron transport, is an appealing, yet underexplored, mode of action due to a dearth of MK-binding molecules. Here we combine sequence-based metagenomic mining with a motif search of bioinformatically predicted natural product structures to identify six biosynthetic gene clusters that we predicted encode MK-binding antibiotics (MBAs). Their predicted products (MBA1-6) were rapidly accessed using a synthetic bioinformatic natural product approach, which relies on bioinformatic structure prediction followed by chemical synthesis. Among these six structurally diverse MBAs, four make up two new MBA structural families. The most potent member of each new family (MBA3, MBA6) proved effective at treating methicillin-resistant Staphylococcus aureus infection in a murine peritonitis-sepsis model. The only conserved feature present in all MBAs is the sequence 'GXLXXXW', which we propose represents a minimum MK-binding motif. Notably, we found that a subset of MBAs were active against Mycobacterium tuberculosis both in vitro and in macrophages. Our findings suggest that naturally occurring MBAs are a structurally diverse and untapped class of mechanistically interesting, in vivo active antibiotics.}, }
@article {pmid34949778, year = {2021}, author = {Shi, ZJ and Dimitrov, B and Zhao, C and Nayfach, S and Pollard, KS}, title = {Fast and accurate metagenotyping of the human gut microbiome with GT-Pro.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {34949778}, issn = {1546-1696}, support = {DMS-1563159//National Science Foundation (NSF)/ ; DMS-1563159//National Science Foundation (NSF)/ ; DMS-1563159//National Science Foundation (NSF)/ ; }, abstract = {Single nucleotide polymorphisms (SNPs) in metagenomics are used to quantify population structure, track strains and identify genetic determinants of microbial phenotypes. However, existing alignment-based approaches for metagenomic SNP detection require high-performance computing and enough read coverage to distinguish SNPs from sequencing errors. To address these issues, we developed the GenoTyper for Prokaryotes (GT-Pro), a suite of methods to catalog SNPs from genomes and use unique k-mers to rapidly genotype these SNPs from metagenomes. Compared to methods that use read alignment, GT-Pro is more accurate and two orders of magnitude faster. Using high-quality genomes, we constructed a catalog of 104 million SNPs in 909 human gut species and used unique k-mers targeting this catalog to characterize the global population structure of gut microbes from 7,459 samples. GT-Pro enables fast and memory-efficient metagenotyping of millions of SNPs on a personal computer.}, }
@article {pmid34947994, year = {2021}, author = {Di Costanzo, F and Di Dato, V and van Zyl, LJ and Cutignano, A and Esposito, F and Trindade, M and Romano, G}, title = {Three Novel Bacteria Associated with Two Centric Diatom Species from the Mediterranean Sea, Thalassiosira rotula and Skeletonema marinoi.}, journal = {International journal of molecular sciences}, volume = {22}, number = {24}, pages = {}, doi = {10.3390/ijms222413199}, pmid = {34947994}, issn = {1422-0067}, support = {690944//Ocean Medicine/ ; PGR00765//Ministry of the Environment and Protection of Land and Sea/ ; UID113128//South African National Research Foundation/ ; }, abstract = {Diatoms are a successful group of microalgae at the base of the marine food web. For hundreds of millions of years, they have shared common habitats with bacteria, which favored the onset of interactions at different levels, potentially driving the synthesis of biologically active molecules. To unveil their presence, we sequenced the genomes of bacteria associated with the centric diatom Thalassiosira rotula from the Gulf of Naples. Annotation of the metagenome and its analysis allowed the reconstruction of three bacterial genomes that belong to currently undescribed species. Their investigation showed the existence of novel gene clusters coding for new polyketide molecules, antibiotics, antibiotic-resistance genes and an ectoine production pathway. Real-time PCR was used to investigate the association of these bacteria with three different diatom clones and revealed their preference for T. rotula FE80 and Skeletonema marinoi FE7, but not S. marinoi FE60 from the North Adriatic Sea. Additionally, we demonstrate that although all three bacteria could be detected in the culture supernatant (free-living), their number is up to 45 times higher in the cell associated fraction, suggesting a close association between these bacteria and their host. We demonstrate that axenic cultures of T. rotula are unable to grow in medium with low salinity (<28 ppt NaCl) whereas xenic cultures can tolerate up to 40 ppt NaCl with concomitant ectoine production, likely by the associated bacteria.}, }
@article {pmid34946803, year = {2021}, author = {Liu, G and Zhang, S and Zhao, X and Li, C and Gong, M}, title = {Advances and Limitations of Next Generation Sequencing in Animal Diet Analysis.}, journal = {Genes}, volume = {12}, number = {12}, pages = {}, doi = {10.3390/genes12121854}, pmid = {34946803}, issn = {2073-4425}, support = {CAFYBB2020ZA004//Fundamental Research Fund of Chinese Academy of Forestry/ ; }, abstract = {Diet analysis is a critical content of animal ecology and the diet analysis methods have been constantly improving and updating. Contrary to traditional methods of high labor intensity and low resolution, the next generation sequencing (NGS) approach has been suggested as a promising tool for dietary studies, which greatly improves the efficiency and broadens the application range. Here we present a framework of adopting NGS and DNA metabarcoding into diet analysis, and discuss the application in aspects of prey taxa composition and structure, intra-specific and inter-specific trophic links, and the effects of animal feeding on environmental changes. Yet, the generation of NGS-based diet data and subsequent analyses and interpretations are still challenging with several factors, making it possible still not as widely used as might be expected. We suggest that NGS-based diet methods must be furthered, analytical pipelines should be developed. More application perspectives, including nutrient geometry, metagenomics and nutrigenomics, need to be incorporated to encourage more ecologists to infer novel insights on they work.}, }
@article {pmid34946202, year = {2021}, author = {Chrzastek, K and Kraberger, S and Schmidlin, K and Fontenele, RS and Kulkarni, A and Chappell, L and Dufour-Zavala, L and Kapczynski, DR and Varsani, A}, title = {Diverse Single-Stranded DNA Viruses Identified in Chicken Buccal Swabs.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/microorganisms9122602}, pmid = {34946202}, issn = {2076-2607}, abstract = {High-throughput sequencing approaches offer the possibility to better understand the complex microbial communities associated with animals. Viral metagenomics has facilitated the discovery and identification of many known and unknown viruses that inhabit mucosal surfaces of the body and has extended our knowledge related to virus diversity. We used metagenomics sequencing of chicken buccal swab samples and identified various small DNA viruses with circular genome organization. Out of 134 putative circular viral-like circular genome sequences, 70 are cressdnaviruses and 26 are microviruses, whilst the remaining 38 most probably represent sub-genomic molecules. The cressdnaviruses found in this study belong to the Circoviridae, Genomoviridae and Smacoviridae families as well as previously described CRESS1 and naryavirus groups. Among these, genomoviruses and smacoviruses were the most prevalent across the samples. Interestingly, we also identified 26 bacteriophages that belong to the Microviridae family, whose members are known to infect enterobacteria.}, }
@article {pmid34946200, year = {2021}, author = {Bordugo, A and Salvetti, E and Rodella, G and Piazza, M and Dianin, A and Amoruso, A and Piacentini, G and Pane, M and Torriani, S and Vitulo, N and Felis, GE}, title = {Assessing Gut Microbiota in an Infant with Congenital Propionic Acidemia before and after Probiotic Supplementation.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/microorganisms9122599}, pmid = {34946200}, issn = {2076-2607}, abstract = {Propionic Acidemia (PA) is a rare inherited metabolic disorder caused by the enzymatic block of propionyl-CoA carboxylase with the consequent accumulation of propionic acid, which is toxic for the brain and cardiac cells. Since a considerable amount of propionate is produced by intestinal bacteria, interest arose in the attempt to reduce propionate-producing bacteria through a monthly antibiotic treatment of metronidazole. In the present study, we investigated the gut microbiota structure of an infant diagnosed at 4 days of life through Expanded Newborn Screening (NBS) and treated the child following international guidelines with a special low-protein diet, specific medications and strict biochemical monitoring. Microbiota composition was assessed during the first month of life, and the presence of Bacteroides fragilis, known to be associated with propionate production, was effectively decreased by metronidazole treatment. After five antibiotic therapy cycles, at 4 months of age, the infant was supplemented with a daily mixture of three bifidobacterial strains, known not to be propionate producers. The supplementation increased the population of bifidobacteria, with Bifidobacterium breve as the dominating species; Ruminococcus gnavus, an acetate and formate producer, was also identified. Metabarcoding analysis, compared with low coverage whole metagenome sequencing, proved to capture all the microbial biodiversity and could be the elected tool for fast and cost-effective monitoring protocols to be implemented in the follow up of rare metabolic disorders such as PA. Data obtained could be a possible starting point to set up tailored microbiota modification treatment studies in the attempt to improve the quality of life of people affected by propionic acidemia.}, }
@article {pmid34946166, year = {2021}, author = {Dedysh, SN and Beletsky, AV and Ivanova, AA and Danilova, OV and Begmatov, S and Kulichevskaya, IS and Mardanov, AV and Ravin, NV}, title = {Peat-Inhabiting Verrucomicrobia of the Order Methylacidiphilales Do Not Possess Methanotrophic Capabilities.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/microorganisms9122566}, pmid = {34946166}, issn = {2076-2607}, support = {19-29-05059//Russian Foundation for Basic Research/ ; none//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Methanotrophic verrucomicrobia of the order Methylacidiphilales are known as extremely acidophilic, thermophilic or mesophilic bacteria that inhabit acidic geothermal ecosystems. The occurrence of verrucomicrobial methanotrophs in other types of acidic environments remains an open question. Notably, Methylacidiphilales-affiliated 16S rRNA gene sequences are commonly retrieved from acidic (pH 3.5-5.5) peatlands. In this study, we compared the patterns of verrucomicrobial diversity in four acidic raised bogs and six neutral fens located in European North Russia. Methylacidiphilales-like 16S rRNA gene reads displaying 83-86% similarity to 16S rRNA gene sequences of currently described verrucomicrobial methanotrophs were recovered exclusively from raised bogs. Laboratory incubation of peat samples with 10% methane for 3 weeks resulted in the pronounced increase of a relative abundance of alphaproteobacterial methanotrophs, while no response was detected for Methylacidiphilales-affiliated bacteria. Three metagenome-assembled genomes (MAGs) of peat-inhabiting Methylacidiphilales bacteria were reconstructed and examined for the presence of genes encoding methane monooxygenase enzymes and autotrophic carbon fixation pathways. None of these genomic determinants were detected in assembled MAGs. Metabolic reconstructions predicted a heterotrophic metabolism, with a potential to hydrolyze several plant-derived polysaccharides. As suggested by our analysis, peat-inhabiting representatives of the Methylacidiphilales are acidophilic aerobic heterotrophs, which comprise a sister family of the methanotrophic Methylacidiphilaceae.}, }
@article {pmid34946163, year = {2021}, author = {Kosaka, S and Nadatani, Y and Higashimori, A and Otani, K and Fujimoto, K and Nagata, Y and Ominami, M and Fukunaga, S and Hosomi, S and Kamata, N and Tanaka, F and Nagami, Y and Taira, K and Imoto, S and Uematsu, S and Watanabe, T and Fujiwara, Y}, title = {Ovariectomy-Induced Dysbiosis May Have a Minor Effect on Bone in Mice.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/microorganisms9122563}, pmid = {34946163}, issn = {2076-2607}, support = {17K15962//JSPS KAKENHI/ ; }, abstract = {We determined the bone mineral density (BMD) and the expression of serum bone formation marker (procollagen type I N-terminal propeptide: PINP) and bone resorption marker (C-terminal telopeptide of collagen: CTX) by ELISA to evaluate ovariectomy-induced osteoporosis in ovariectomized (OVX) mice. The intestinal microbiota of the mice was assessed using 16S rRNA gene sequencing. OVX mice exhibited a lower BMD of 87% with higher serum levels of CTX and PINP compared to sham-operated (sham) mice. The cecum microbiome of OVX mice showed lower bacterial diversity than that of sham mice. TNFα mRNA levels in the colon were 1.6 times higher, and zonula occludens-1 mRNA and protein expression were lower in OVX mice than in sham mice, suggesting that ovariectomy induced inflammation and increased intestinal permeability. Next, we used antibiotic treatment followed by fecal microbiota transplantation (FMT) to remodel the gut microbiota in the OVX mice. A decrease in PINP was observed in antibiotic-treated mice, while there was no change in BMD or CTX between mice with and without antibiotic treatment. Oral transplantation of the luminal cecal content of OVX or sham mice to antibiotic-treated mice did not affect the BMD or PINP and CTX expression. Additionally, transplantation of the luminal contents of OVX or sham mice to antibiotic-treated OVX mice had similar effects on BMD, PINP, and CTX. In conclusion, although ovariectomy induces dysbiosis in the colon, the changes in the gut microbiota may only have a minor role in ovariectomy-induced osteoporosis.}, }
@article {pmid34946144, year = {2021}, author = {Nielsen, KL and Olsen, MH and Pallejá, A and Ebdrup, SR and Sørensen, N and Lukjancenko, O and Marvig, RL and Møller, K and Frimodt-Møller, N and Hertz, FB}, title = {Microbiome Compositions and Resistome Levels after Antibiotic Treatment of Critically Ill Patients: An Observational Cohort Study.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/microorganisms9122542}, pmid = {34946144}, issn = {2076-2607}, support = {NA//Mica Foundation/ ; }, abstract = {Hospitalization and treatment with antibiotics increase the risk of acquiring multidrug-resistant bacteria due to antibiotic-mediated changes in patient microbiota. This study aimed to investigate how broad- and narrow-spectrum antibiotics affect the gut microbiome and the resistome in antibiotic naïve patients during neurointensive care. Patients admitted to the neurointensive care unit were treated with broad-spectrum (meropenem or piperacillin/tazobactam) or narrow-spectrum antibiotic treatment (including ciprofloxacin, cefuroxime, vancomycin and dicloxacillin) according to clinical indications. A rectal swab was collected from each patient before and after 5-7 days of antibiotic therapy (N = 34), respectively. Shotgun metagenomic sequencing was performed and the composition of metagenomic species (MGS) was determined. The resistome was characterized with CARD RGI software and the CARD database. As a measure for selection pressure in the patient, we used the sum of the number of days with each antibiotic (antibiotic days). We observed a significant increase in richness and a tendency for an increase in the Shannon index after narrow-spectrum treatment. For broad-spectrum treatment the effect was more diverse, with some patients increasing and some decreasing in richness and Shannon index. This was studied further by comparison of patients who had gained or lost >10 MGS, respectively. Selection pressure was significantly higher in patients with decreased richness and a decreased Shannon index who received the broad treatment. A decrease in MGS richness was significantly correlated to the number of drugs administered and the selection pressure in the patient. Bray-Curtis dissimilarities were significant between the pre- and post-treatment of samples in the narrow group, indicating that the longer the narrow-spectrum treatment, the higher the differences between the pre- and the post-treatment microbial composition. We did not find significant differences between pre- and post-treatment for both antibiotic spectrum treatments; however, we observed that most of the antibiotic class resistance genes were higher in abundance in post-treatment after broad-spectrum treatment.}, }
@article {pmid34946095, year = {2021}, author = {Xiang, B and Zhao, L and Zhang, M}, title = {Metagenome-Scale Metabolic Network Suggests Folate Produced by Bifidobacterium longum Might Contribute to High-Fiber-Diet-Induced Weight Loss in a Prader-Willi Syndrome Child.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/microorganisms9122493}, pmid = {34946095}, issn = {2076-2607}, abstract = {Gut-microbiota-targeted nutrition intervention has achieved success in the management of obesity, but its underlying mechanism still needs extended exploration. An obese Prader-Willi syndrome boy lost 25.8 kg after receiving a high-fiber dietary intervention for 105 days. The fecal microbiome sequencing data taken from the boy on intervention days 0, 15, 30, 45, 60, 75, and 105, along with clinical indexes, were used to construct a metagenome-scale metabolic network. Firstly, the abundances of the microbial strains were obtained by mapping the sequencing reads onto the assembly of gut organisms through use of reconstruction and analysis (AGORA) genomes. The nutritional components of the diet were obtained through the Virtual Metabolic Human database. Then, a community model was simulated using the Microbiome Modeling Toolbox. Finally, the significant Spearman correlations among the metabolites and the clinical indexes were screened and the strains that were producing these metabolites were identified. The high-fiber diet reduced the overall amount of metabolite secretions, but the secretions of folic acid derivatives by Bifidobacterium longum strains were increased and were significantly relevant to the observed weight loss. Reduced metabolites might also have directly contributed to the weight loss or indirectly contribute by enhancing leptin and decreasing adiponectin. Metagenome-scale metabolic network technology provides a cost-efficient solution for screening the functional microbial strains and metabolic pathways that are responding to nutrition therapy.}, }
@article {pmid34946078, year = {2021}, author = {Van Bel, M and Fisher, AE and Ball, L and Columbus, JT and Berlemont, R}, title = {Phylosymbiosis in the Rhizosphere Microbiome Extends to Nitrogen Cycle Functional Potential.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/microorganisms9122476}, pmid = {34946078}, issn = {2076-2607}, abstract = {Most plants rely on specialized root-associated microbes to obtain essential nitrogen (N), yet not much is known about the evolutionary history of the rhizosphere-plant interaction. We conducted a common garden experiment to investigate the plant root-rhizosphere microbiome association using chloridoid grasses sampled from around the world and grown from seed in a greenhouse. We sought to test whether plants that are more closely related phylogenetically have more similar root bacterial microbiomes than plants that are more distantly related. Using metagenome sequencing, we found that there is a conserved core and a variable rhizosphere bacterial microbiome across the chloridoid grasses. Additionally, phylogenetic distance among the host plant species was correlated with bacterial community composition, suggesting the plant hosts prefer specific bacterial lineages. The functional potential for N utilization across microbiomes fluctuated extensively and mirrored variation in the microbial community composition across host plants. Variation in the bacterial potential for N fixation was strongly affected by the host plants' phylogeny, whereas variation in N recycling, nitrification, and denitrification was unaffected. This study highlights the evolutionary linkage between the N fixation traits of the microbial community and the plant host and suggests that not all functional traits are equally important for plant-microbe associations.}, }
@article {pmid34946026, year = {2021}, author = {Nõlvak, H and Dang, NP and Truu, M and Peeb, A and Tiirik, K and O'Sadnick, M and Truu, J}, title = {Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/microorganisms9122425}, pmid = {34946026}, issn = {2076-2607}, support = {PRG548//Estonian Research Council/ ; N.679266//EU Horizon 2020 Programme/ ; }, abstract = {The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure, dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater. The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently, the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation. The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe.}, }
@article {pmid34945537, year = {2021}, author = {Su, H and Zhang, Q and Yu, K and Lu, C and Xiao, Z and Huang, Q and Wang, S and Wang, Y and Wang, G and Liang, J}, title = {A Novel Neutral and Mesophilic β-Glucosidase from Coral Microorganisms for Efficient Preparation of Gentiooligosaccharides.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/foods10122985}, pmid = {34945537}, issn = {2304-8158}, support = {42030502//National Natural Science Foundation of China/ ; }, abstract = {β-glucosidases can produce gentiooligosaccharides that are lucrative and promising for the prebiotic and alternative food industries. However, the commercial production of gentiooligosaccharides using β-glucosidase is challenging, as this process is limited by the need for high thermal energy and increasing demand for the enzyme. Here, a putative β-glucosidase gene, selected from the coral microbial metagenome, was expressed in Escherichia coli. Reverse hydrolysis of glucose by Blg163 at pH 7.0 and 40 °C achieved a gentiooligosaccharide yield of 43.02 ± 3.20 g·L-1 at a conversion rate of 5.38 ± 0.40%. Transglycosylation of mixed substrates, glucose and cellobiose, by Blg163 consumed 21.6 U/0.5 g glucose/g cellobiose, achieving a gentiooligosaccharide yield of 70.34 ± 2.20 g·L-1 at a conversion rate of 15.63%, which is close to the highest yield reported in previous findings. Blg163-mediated synthesis of gentiooligosaccharides is the mildest reaction and the lowest β-glucosidase consumption reported to date.}, }
@article {pmid34943919, year = {2021}, author = {Misztak, AE and Waleron, M and Furmaniak, M and Waleron, MM and Bazhenova, O and Daroch, M and Waleron, KF}, title = {Comparative Genomics and Physiological Investigation of a New Arthrospira/Limnospira Strain O9.13F Isolated from an Alkaline, Winter Freezing, Siberian Lake.}, journal = {Cells}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/cells10123411}, pmid = {34943919}, issn = {2073-4409}, abstract = {Cyanobacteria from the genus Arthrospira/Limnospira are considered haloalkalotolerant organisms with optimal growth temperatures around 35 °C. They are most abundant in soda lakes in tropical and subtropical regions. Here, we report the comprehensive genome-based characterisation and physiological investigation of the new strain O9.13F that was isolated in a temperate climate zone from the winter freezing Solenoye Lake in Western Siberia. Based on genomic analyses, the Siberian strain belongs to the Arthrospira/Limnospira genus. The described strain O9.13F showed the highest relative growth index upon cultivation at 20 °C, lower than the temperature 35 °C reported as optimal for the Arthrospira/Limnospira strains. We assessed the composition of fatty acids, proteins and photosynthetic pigments in the biomass of strain O9.13F grown at different temperatures, showing its potential suitability for cultivation in a temperate climate zone. We observed a decrease of gamma-linolenic acid favouring palmitic acid in the case of strain O9.13F compared to tropical strains. Comparative genomics showed no unique genes had been found for the Siberian strain related to its tolerance to low temperatures. In addition, this strain does not possess a different set of genes associated with the salinity stress response from those typically found in tropical strains. We confirmed the absence of plasmids and functional prophage sequences. The genome consists of a 4.94 Mbp with a GC% of 44.47% and 5355 encoded proteins. The Arthrospira/Limnospira strain O9.13F presented in this work is the first representative of a new clade III based on the 16S rRNA gene, for which a genomic sequence is available in public databases (PKGD00000000).}, }
@article {pmid34943721, year = {2021}, author = {Fésüs, A and Benkő, R and Matuz, M and Kungler-Gorácz, O and Fésüs, MÁ and Bazsó, T and Csernátony, Z and Kardos, G}, title = {The Effect of Pharmacist-Led Intervention on Surgical Antibacterial Prophylaxis (SAP) at an Orthopedic Unit.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/antibiotics10121509}, pmid = {34943721}, issn = {2079-6382}, abstract = {Perioperative antibiotic use is a common reason for antibiotic misuse. Evidence suggests that adherence to SAP guidelines may improve outcomes. The purpose of this study was to analyze the impact of pharmacist-led antibiotic stewardship interventions on SAP guideline compliance. The study was conducted at an Orthopedic Department of a tertiary care medical center. SAP compliance and antibiotic exposure in the pre-intervention and intervention period was compared using chi-square, Fisher exact, and Mann-Whitney tests, as appropriate. Prophylactic antibiotic use in orthopedic joint arthroplasties (overall guideline adherence: agent, dose, frequency, duration), clinical outcomes (length of stay-LOS, number of surgical site infections-SSIs), antibiotic exposure and direct antibiotic costs were compared between pre-intervention and intervention periods. Significant improvement in mean SAP duration (by 42.9%, 4.08 ± 2.08 vs. 2.08 ± 1.90 days, p ˂ 0.001), and overall guideline adherence regarding antibiotic use (by 56.2%, from 2% to 58.2%, p ˂ 0.001) were observed. A significant decrease was observed in antibiotic exposure in SAP (by 41%, from 6.07 ± 0.05 to 3.58 ± 4.33 DDD/patient, p ˂ 0.001), average prophylactic antibiotic cost (by 54.8%, 9278.79 ± 6094.29 vs. 3598.16 ± 3354.55 HUF/patient), and mean LOS (by 37.2%, from 11.22 ± 6.96 to 7.62 ± 3.02 days, p < 0.001); and a slight decrease in the number of confirmed SSIs was found between the two periods (by 1.8%, from 3% to 1.2%, p = 0.21). Continuous presence of the clinical pharmacist led to significant improvement in SAP guideline adherence, which was accompanied by decreased antibiotic exposure and cost.}, }
@article {pmid34943176, year = {2021}, author = {Liu, D and Bhople, P and Keiblinger, KM and Wang, B and An, S and Yang, N and Chater, CCC and Yu, F}, title = {Soil Rehabilitation Promotes Resilient Microbiome with Enriched Keystone Taxa than Agricultural Infestation in Barren Soils on the Loess Plateau.}, journal = {Biology}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/biology10121261}, pmid = {34943176}, issn = {2079-7737}, support = {A314021402-2002//Open-Funds of Scientific Research Programs of State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau/ ; XDA26050302//"Strategic Priority Research Program" of the Chinese Academy of Sciences/ ; E13A44//Basic Research - General Program of Yunnan Province/ ; }, abstract = {Drylands provide crucial ecosystem and economic services across the globe. In barren drylands, keystone taxa drive microbial structure and functioning in soil environments. In the current study, the Chinese Loess plateau's agricultural (AL) and twenty-year-old rehabilitated lands (RL) provided a unique opportunity to investigate land-use-mediated effects on barren soil keystone bacterial and fungal taxa. Therefore, soils from eighteen sites were collected for metagenomic sequencing of bacteria specific 16S rRNA and fungi specific ITS2 regions, respectively, and to conduct molecular ecological networks and construct microbial OTU-based correlation matrices. In RL soils we found a more complex bacterial network represented by a higher number of nodes and links, with a link percentage of 77%, and a lower number of nodes and links for OTU-based fungal networks compared to the AL soils. A higher number of keystone taxa was observed in the RL (66) than in the AL (49) soils, and microbial network connectivity was positively influenced by soil total nitrogen and microbial biomass carbon contents. Our results indicate that plant restoration and the reduced human interventions in RL soils could guide the development of a better-connected microbial network and ensure sufficient nutrient circulation in barren soils on the Loess plateau.}, }
@article {pmid34630388, year = {2021}, author = {Kong, L and Wang, Z and Xiao, C and Zhu, Q and Song, Z}, title = {Glycerol Monolaurate Ameliorated Intestinal Barrier and Immunity in Broilers by Regulating Intestinal Inflammation, Antioxidant Balance, and Intestinal Microbiota.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {713485}, pmid = {34630388}, issn = {1664-3224}, mesh = {Animals ; Antioxidants/*metabolism ; Chickens ; Cytokines/biosynthesis ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Immunity, Mucosal/*drug effects ; Immunoglobulin G/blood/immunology ; Intestinal Mucosa/*immunology/*metabolism/pathology ; Laurates/*pharmacology ; Metagenome ; Metagenomics/methods ; Monoglycerides/*pharmacology ; Mucins/genetics/metabolism ; }, abstract = {This study was conducted to investigate the impact of glycerol monolaurate (GML) on performance, immunity, intestinal barrier, and cecal microbiota in broiler chicks. A total of 360 one-day-old broilers (Arbor Acres) with an average weight of 45.7 g were randomly allocated to five dietary groups as follows: basal diet and basal diets complemented with 300, 600, 900, or 1200 mg/kg GML. Samples were collected at 7 and 14 days of age. Results revealed that feed intake increased (P < 0.05) after 900 and 1200 mg/kg GML were administered during the entire 14-day experiment period. Dietary GML decreased (P < 0.05) crypt depth and increased the villus height-to-crypt depth ratio of the jejunum. In the serum and jejunum, supplementation with more than 600 mg/kg GML reduced (P < 0.05) interleukin-1β, tumor necrosis factor-α, and malondialdehyde levels and increased (P < 0.05) the levels of immunoglobulin G, jejunal mucin 2, total antioxidant capacity, and total superoxide dismutase. GML down-regulate (P < 0.05) jejunal interleukin-1β and interferon-γ expression and increased (P < 0.05) the mRNA level of zonula occludens 1 and occludin. A reduced (P < 0.05) expression of toll-like receptor 4 and nuclear factor kappa-B was shown in GML-treated groups. In addition, GML modulated the composition of the cecal microbiota of the broilers, improved (P < 0.05) microbial diversity, and increased (P < 0.05) the abundance of butyrate-producing bacteria. Spearman's correlation analysis revealed that the genera Barnesiella, Coprobacter, Lachnospiraceae, Faecalibacterium, Bacteroides, Odoriacter, and Parabacteroides were related to inflammation and intestinal integrity. In conclusion, GML ameliorated intestinal morphology and barrier function in broiler chicks probably by regulating intestinal immune and antioxidant balance, as well as intestinal microbiota.}, }
@article {pmid34611253, year = {2021}, author = {Kačírová, J and Maďari, A and Mucha, R and Fecskeová, LK and Mujakic, I and Koblížek, M and Nemcová, R and Maďar, M}, title = {Study of microbiocenosis of canine dental biofilms.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19776}, pmid = {34611253}, issn = {2045-2322}, mesh = {Animals ; Bacteria/classification/genetics ; *Biofilms ; Dogs ; Metagenome ; Metagenomics/methods ; *Microbiota ; Periodontium/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tooth/*microbiology ; }, abstract = {Dental biofilm is a complex microbial community influenced by many exogenous and endogenous factors. Despite long-term studies, its bacterial composition is still not clearly understood. While most of the research on dental biofilms was conducted in humans, much less information is available from companion animals. In this study, we analyzed the composition of canine dental biofilms using both standard cultivation on solid media and amplicon sequencing, and compared the two approaches. The 16S rRNA gene sequences were used to define the bacterial community of canine dental biofilm with both, culture-dependent and culture-independent methods. After DNA extraction from each sample, the V3-V4 region of the 16S rRNA gene was amplified and sequenced via Illumina MiSeq platform. Isolated bacteria were identified using universal primers and Sanger sequencing. Representatives of 18 bacterial genera belonging to 5 phyla were isolated from solid media. Amplicon sequencing largely expanded this information identifying in total 284 operational taxonomic units belonging to 10 bacterial phyla. Amplicon sequencing revealed much higher diversity of bacteria in the canine dental biofilms, when compared to standard cultivation approach. In contrast, cultured representatives of several bacterial families were not identified by amplicon sequencing.}, }
@article {pmid34599245, year = {2021}, author = {Ikegami, H and Noguchi, S and Fukuda, K and Akata, K and Yamasaki, K and Kawanami, T and Mukae, H and Yatera, K}, title = {Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19534}, pmid = {34599245}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Disease Susceptibility ; Female ; Gene Library ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Respiratory Mucosa/*microbiology ; Respiratory Tract Infections/diagnosis/*etiology ; Retrospective Studies ; }, abstract = {Next-generation sequencing (NGS) technologies have been applied in bacterial flora analysis. However, there is no standardized protocol, and the optimal clustering threshold for estimating bacterial species in respiratory infection specimens is unknown. This study was conducted to investigate the optimal threshold for clustering 16S ribosomal RNA gene sequences into operational taxonomic units (OTUs) by comparing the results of NGS technology with those of the Sanger method, which has a higher accuracy of sequence per single read than NGS technology. This study included 45 patients with pneumonia with aspiration risks and 35 patients with lung abscess. Compared to Sanger method, the concordance rates of NGS technology (clustered at 100%, 99%, and 97% homology) with the predominant phylotype were 78.8%, 71.3%, and 65.0%, respectively. With respect to the specimens dominated by the Streptococcus mitis group, containing several important causative agents of pneumonia, Bray Curtis dissimilarity revealed that the OTUs obtained at 100% clustering threshold (versus those obtained at 99% and 97% thresholds; medians of 0.35, 0.69, and 0.71, respectively) were more similar to those obtained by the Sanger method, with statistical significance (p < 0.05). Clustering with 100% sequence identity is necessary when analyzing the microbiota of respiratory infections using NGS technology.}, }
@article {pmid33542492, year = {2021}, author = {Jones-Freeman, B and Chonwerawong, M and Marcelino, VR and Deshpande, AV and Forster, SC and Starkey, MR}, title = {The microbiome and host mucosal interactions in urinary tract diseases.}, journal = {Mucosal immunology}, volume = {14}, number = {4}, pages = {779-792}, pmid = {33542492}, issn = {1935-3456}, mesh = {Animals ; Disease Management ; Disease Susceptibility ; Feedback, Physiological ; Gastrointestinal Microbiome ; Homeostasis ; *Host Microbial Interactions ; *Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mucous Membrane/*microbiology ; Organ Specificity ; Urinary Tract Infections/diagnosis/*etiology/therapy ; }, abstract = {The urinary tract consists of the bladder, ureters, and kidneys, and is an essential organ system for filtration and excretion of waste products and maintaining systemic homeostasis. In this capacity, the urinary tract is impacted by its interactions with other mucosal sites, including the genitourinary and gastrointestinal systems. Each of these sites harbors diverse ecosystems of microbes termed the microbiota, that regulates complex interactions with the local and systemic immune system. It remains unclear whether changes in the microbiota and associated metabolites may be a consequence or a driver of urinary tract diseases. Here, we review the current literature, investigating the impact of the microbiota on the urinary tract in homeostasis and disease including urinary stones, acute kidney injury, chronic kidney disease, and urinary tract infection. We propose new avenues for exploration of the urinary microbiome using emerging technology and discuss the potential of microbiome-based medicine for urinary tract conditions.}, }
@article {pmid34941962, year = {2021}, author = {Schiffer, JA and Stumbur, SV and Seyedolmohadesin, M and Xu, Y and Serkin, WT and McGowan, NG and Banjo, O and Torkashvand, M and Lin, A and Hosea, CN and Assié, A and Samuel, BS and O'Donnell, MP and Venkatachalam, V and Apfeld, J}, title = {Modulation of sensory perception by hydrogen peroxide enables Caenorhabditis elegans to find a niche that provides both food and protection from hydrogen peroxide.}, journal = {PLoS pathogens}, volume = {17}, number = {12}, pages = {e1010112}, doi = {10.1371/journal.ppat.1010112}, pmid = {34941962}, issn = {1553-7374}, abstract = {Hydrogen peroxide (H2O2) is the most common chemical threat that organisms face. Here, we show that H2O2 alters the bacterial food preference of Caenorhabditis elegans, enabling the nematodes to find a safe environment with food. H2O2 induces the nematodes to leave food patches of laboratory and microbiome bacteria when those bacterial communities have insufficient H2O2-degrading capacity. The nematode's behavior is directed by H2O2-sensing neurons that promote escape from H2O2 and by bacteria-sensing neurons that promote attraction to bacteria. However, the input for H2O2-sensing neurons is removed by bacterial H2O2-degrading enzymes and the bacteria-sensing neurons' perception of bacteria is prevented by H2O2. The resulting cross-attenuation provides a general mechanism that ensures the nematode's behavior is faithful to the lethal threat of hydrogen peroxide, increasing the nematode's chances of finding a niche that provides both food and protection from hydrogen peroxide.}, }
@article {pmid34941754, year = {2021}, author = {Kim, JW and Hong, YK and Kim, HS and Oh, EJ and Park, YH and Kim, SC}, title = {Metagenomic Analysis for Evaluating Change in Bacterial Diversity in TPH-Contaminated Soil after Soil Remediation.}, journal = {Toxics}, volume = {9}, number = {12}, pages = {}, doi = {10.3390/toxics9120319}, pmid = {34941754}, issn = {2305-6304}, support = {2020002480005//Ministry of Environment/ ; }, abstract = {Soil washing and landfarming processes are widely used to remediate total petroleum hydrocarbon (TPH)-contaminated soil, but the impact of these processes on soil bacteria is not well understood. Four different states of soil (uncontaminated soil (control), TPH-contaminated soil (CS), after soil washing (SW), and landfarming (LF)) were collected from a soil remediation facility to investigate the impact of TPH and soil remediation processes on soil bacterial populations by metagenomic analysis. Results showed that TPH contamination reduced the operational taxonomic unit (OTU) number and alpha diversity of soil bacteria. Compared to SW and LF remediation techniques, LF increased more bacterial richness and diversity than SW, indicating that LF is a more effective technique for TPH remediation in terms of microbial recovery. Among different bacterial species, Proteobacteria were the most abundant in all soil groups followed by Actinobacteria, Acidobacteria, and Firmicutes. For each soil group, the distribution pattern of the Proteobacteria class was different. The most abundant classed were Alphaproteobacteria (16.56%) in uncontaminated soils, Deltaproteobacteria (34%) in TPH-contaminated soils, Betaproteobacteria (24%) in soil washing, and Gammaproteobacteria (24%) in landfarming, respectively. TPH-degrading bacteria were detected from soil washing (23%) and TPH-contaminated soils (21%) and decreased to 12% in landfarming soil. These results suggest that soil pollution can change the diversity of microbial groups and different remediation techniques have varied effective ranges for recovering bacterial communities and diversity. In conclusion, the landfarming process of TPH remediation is more advantageous than soil washing from the perspective of bacterial ecology.}, }
@article {pmid34941731, year = {2021}, author = {Hu, D and Giesy, JP and Guo, M and Ung, WK and Kong, Y and Mok, KM and Lee, SM}, title = {Temporal Patterns of Bacterial and Viral Communities during Algae Blooms of a Reservoir in Macau.}, journal = {Toxins}, volume = {13}, number = {12}, pages = {}, doi = {10.3390/toxins13120894}, pmid = {34941731}, issn = {2072-6651}, support = {FDCT/069/2014/A2//Fundo para lo Desenvolvimento das Ciências e da Tecnologia/ ; GDT20143200016//State Administration of Foreign Experts Affairs, the P.R. China to Nanjing University and the Einstein Professor Program of the Chinese Academy of Sciences/ ; }, abstract = {Compositions of microbial communities associated with blooms of algae in a storage reservoir in Macau, China were investigated between 2013 and 2016. Algae were enumerated by visible light microscopy. Profiles of organisms in water were examined by 16S rRNA sequences and viral metagenomics, based on next generation sequencing. Results of 16S rRNA sequencing indicated that majority of the identified organisms were bacteria closely related to Proteobacteria, Cyanobacteria, Verrucomicrobia, Bacteroidetes, and Actinobacteria. Metagenomics sequences demonstrated that the dominant virus was Phycodnavirus, accounting for 70% of the total population. Patterns of relative numbers of bacteria in the microbial community and their temporal changes were determined through alpha diversity indices, principal coordinates analysis (PCoA), relative abundance, and visualized by Venn diagrams. Ways in which the bacterial and viral communities are influenced by various water-related variables were elucidated based on redundancy analysis (RDA). Relationships of the relative numbers of bacteria with trophic status in a reservoir used for drinking water in Macau, provided insight into associations of Phycodnavirus and Proteobacteria with changes in blooms of algae.}, }
@article {pmid34940575, year = {2021}, author = {Jhang, SY and Lee, SH and Lee, EB and Choi, JH and Bang, S and Jeong, M and Jang, HH and Kim, HJ and Lee, HJ and Jeong, HC and Lee, SJ}, title = {Effects of Platycodon grandiflorum on Gut Microbiome and Immune System of Immunosuppressed Mouse.}, journal = {Metabolites}, volume = {11}, number = {12}, pages = {}, doi = {10.3390/metabo11120817}, pmid = {34940575}, issn = {2218-1989}, support = {PJ01586301//Rural Development Administration/ ; }, abstract = {Platycodon grandiflorum (PG) is a perennial plant that has been used as a traditional remedy to control immune-related diseases. PG was steamed and dried to improve its taste (PGS). The aim of the study was to investigate the effects of PG and PGS (PG-diets) on the gut microbiome and immune system. We treated PG-diets to immunosuppressed mice via cyclophosphamide (CPA) injection. After two weeks of the supplement, we evaluated specific genera related to body weight and serum immunoglobulin levels and analyzed 16S rRNA sequencing and metagenomics statistical analysis. PG-diets groups showed an increased abundance of microorganisms in immunodeficient mice compared to the control group (NC). Moreover, Akkermansia significantly decreased in response to the CPA in the NC group at the genus level, whereas its abundance increased in the PG-diets groups. We also found that the modulation of the gut microbiome by PG-diets was correlated with body weight, IgA, and IgM levels. The results demonstrate that PG-diets may improve the health benefits of immunosuppressed mice by altering the gut microbiome, though not much difference was found between PG and PGS treatments. Finally, this is the first study showing the effects of PGS-diets on the gut microbiome and immune system as a potential nourishing immunity supplement.}, }
@article {pmid34939905, year = {2021}, author = {Cao, M and Peng, Q and Wei, ZG and Liu, F and Hou, YF}, title = {EdClust: A heuristic sequence clustering method with higher sensitivity.}, journal = {Journal of bioinformatics and computational biology}, volume = {}, number = {}, pages = {2150036}, doi = {10.1142/S0219720021500360}, pmid = {34939905}, issn = {1757-6334}, abstract = {The development of high-throughput technologies has produced increasing amounts of sequence data and an increasing need for efficient clustering algorithms that can process massive volumes of sequencing data for downstream analysis. Heuristic clustering methods are widely applied for sequence clustering because of their low computational complexity. Although numerous heuristic clustering methods have been developed, they suffer from two limitations: overestimation of inferred clusters and low clustering sensitivity. To address these issues, we present a new sequence clustering method (edClust) based on Edlib, a C/C[Formula: see text] library for fast, exact semi-global sequence alignment to group similar sequences. The new method edClust was tested on three large-scale sequence databases, and we compared edClust to several classic heuristic clustering methods, such as UCLUST, CD-HIT, and VSEARCH. Evaluations based on the metrics of cluster number and seed sensitivity (SS) demonstrate that edClust can produce fewer clusters than other methods and that its SS is higher than that of other methods. The source codes of edClust are available from https://github.com/zhang134/EdClust.git under the GNU GPL license.}, }
@article {pmid34939673, year = {2021}, author = {Rahaman, MM and Sarkar, MMH and Rahman, MS and Islam, MR and Islam, I and Saha, O and Akter, S and Banu, TA and Jahan, I and Habib, MA and Goswami, B and Bari, L and Malek, MA and Khan, MS}, title = {Genomic characterization of the dominating Beta variant carrying vaccinated (Oxford-AstraZeneca) and non-vaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole genome approach.}, journal = {Journal of medical virology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jmv.27537}, pmid = {34939673}, issn = {1096-9071}, abstract = {Bangladesh experiences a second wave of COVID-19 since March 2021, despite the nationwide vaccination drive with ChAdOx1 (Oxford-AstraZeneca) vaccine from early February 2021. Here, we characterized 19 nasopharyngeal swab (NPS) samples from COVID-19 suspect patients using genomic and metagenomic approach. Screening for SARS-CoV-2 by RT-PCR and metagenomic sequencing revealed 17 samples of COVID-19 positive (vaccinated=10, non-vaccinated=7) and 2 samples of COVID-19 negative. We did not find any significant correlation between associated factors including vaccination status, age or sex of the patients, diversity or abundance of the co-infected organisms/pathogens, and the abundance of SARS-CoV-2. Though the first wave of the pandemic was dominated by clade 20B, Beta,V2 (South African variant) dominated the second wave (January 2021 to May 2021), while the third wave (May 2021 to September 2021) was responsible for Delta variants of the epidemic in Bangladesh including both vaccinated and unvaccinated infections. Noteworthy, the RBD region of S protein of all the isolates harbored similar substitutions including K417N, E484K and N501Y that signify the Beta, while D614G, D215G, D80A, A67V, L18F and A701V substitutions were commonly found in the non-RBD region of Spike proteins. ORF7b and ORF3a genes underwent a positive selection (dN/dS ratio 1.77 and 1.24, respectively), while the overall S protein of the Bangladeshi SARS-CoV-2 isolates underwent negative selection pressure (dN/dS=0.621). Furthermore, we found different bacterial co-infection like Streptococcus agalactiae, Neisseria meningitidis, Elizabethkingia anophelis, Stenotrophomonas maltophilia, Klebsiella pneumoni and Pseudomonas plecoglossicida, expressing a number of antibiotic resistance genes such as tetA and tetM. Overall, this approach provides valuable insights on the SARS-CoV-2 genomes and microbiome composition from both vaccinated and non-vaccinated patients in Bangladesh. This article is protected by copyright. All rights reserved.}, }
@article {pmid34939130, year = {2021}, author = {Trzebny, A and Slodkowicz-Kowalska, A and Björkroth, J and Dabert, M}, title = {Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34939130}, issn = {1432-184X}, support = {2020/37/N/NZ8/01735//Narodowe Centrum Nauki/ ; 05/IDUB/2019/94//Initiative of Excellence - Research University at Adam Mickiewicz University, Poznan, Poland/ ; }, abstract = {The animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.}, }
@article {pmid34938418, year = {2021}, author = {Serrano-Gómez, G and Mayorga, L and Oyarzun, I and Roca, J and Borruel, N and Casellas, F and Varela, E and Pozuelo, M and Machiels, K and Guarner, F and Vermeire, S and Manichanh, C}, title = {Dysbiosis and relapse-related microbiome in inflammatory bowel disease: A shotgun metagenomic approach.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {6481-6489}, doi = {10.1016/j.csbj.2021.11.037}, pmid = {34938418}, issn = {2001-0370}, abstract = {Crohn's disease (CD) and ulcerative colitis (UC), the two main forms of inflammatory bowel disease (IBD), affect several million people worldwide. CD and UC are characterized by periods of clinical remission and relapse. Although IBD patients present chronic alterations of the gut microbiome, called dysbiosis, little attention has been devoted to the relapse-related microbiome. To address this gap, we generated shotgun metagenomic data from the stools of two European cohorts-134 Spanish (followed up for one year) and 49 Belgian (followed up for 6 months) subjects-to characterize the microbial taxonomic and metabolic profiles present. To assess the predictive value of microbiome data, we added the taxonomic profiles generated from a previous study of 130 Americans. Our results revealed that CD was more dysbiotic than UC compared to healthy controls (HC) and that strategies for energy extraction and propionate production were different in CD compared to UC and HC. Remarkably, CD and UC relapses were not associated with alpha- or beta-diversity, or with a dysbiotic score. However, CD relapse was linked to alterations at the species and metabolic pathway levels, including those involved in propionate production. The random forest method using taxonomic profiles allowed the prediction of CD vs. non-CD with an AUC = 0.938, UC vs. HC with an AUC = 0.646, and CD relapse vs. remission with an AUC = 0.769. Our study validates previous taxonomic findings, points to different relapse-related growth and defence mechanisms in CD compared to UC and HC and provides biomarkers to discriminate IBD subtypes and predict disease activity.}, }
@article {pmid34938409, year = {2021}, author = {Fernandez-Lopez, L and Sanchez-Carrillo, S and García-Moyano, A and Borchert, E and Almendral, D and Alonso, S and Cea-Rama, I and Miguez, N and Larsen, Ø and Werner, J and Makarova, KS and Plou, FJ and Dahlgren, TG and Sanz-Aparicio, J and Hentschel, U and Bjerga, GEK and Ferrer, M}, title = {The bone-degrading enzyme machinery: From multi-component understanding to the treatment of residues from the meat industry.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {6328-6342}, doi = {10.1016/j.csbj.2021.11.027}, pmid = {34938409}, issn = {2001-0370}, abstract = {Many microorganisms feed on the tissue and recalcitrant bone materials from dead animals, however little is known about the collaborative effort and characteristics of their enzymes. In this study, microbial metagenomes from symbionts of the marine bone-dwelling worm Osedax mucofloris, and from microbial biofilms growing on experimentally deployed bone surfaces were screened for specialized bone-degrading enzymes. A total of 2,043 taxonomically (closest match within 40 phyla) and functionally (1 proteolytic and 9 glycohydrolytic activities) diverse and non-redundant sequences (median pairwise identity of 23.6%) encoding such enzymes were retrieved. The taxonomic assignation and the median identity of 72.2% to homologous proteins reflect microbial and functional novelty associated to a specialized bone-degrading marine community. Binning suggests that only one generalist hosting all ten targeted activities, working in synergy with multiple specialists hosting a few or individual activities. Collagenases were the most abundant enzyme class, representing 48% of the total hits. A total of 47 diverse enzymes, representing 8 hydrolytic activities, were produced in Escherichia coli, whereof 13 were soluble and active. The biochemical analyses revealed a wide range of optimal pH (4.0-7.0), optimal temperature (5-65 °C), and of accepted substrates, specific to each microbial enzyme. This versatility may contribute to a high environmental plasticity of bone-degrading marine consortia that can be confronted to diverse habitats and bone materials. Through bone-meal degradation tests, we further demonstrated that some of these enzymes, particularly those from Flavobacteriaceae and Marinifilaceae, may be an asset for development of new value chains in the biorefinery industry.}, }
@article {pmid34938279, year = {2021}, author = {Singh, NK and Lavire, C and Nesme, J and Vial, L and Nesme, X and Mason, CE and Lassalle, F and Venkateswaran, K}, title = {Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {765943}, doi = {10.3389/fmicb.2021.765943}, pmid = {34938279}, issn = {1664-302X}, abstract = {Strains of Agrobacterium genomospecies 3 (i.e., genomovar G3 of the Agrobacterium tumefaciens species complex) have been previously isolated from diverse environments, including in association with plant roots, with algae, as part of a lignocellulose degrading community, from a hospital environment, as a human opportunistic pathogen, or as reported in this study, from a surface within the International Space Station. Polyphasic taxonomic methods revealed the relationship of Agrobacterium G3 strains to other Agrobacterium spp., which supports the description of a novel species. The G3 strains tested (n = 9) were phenotypically distinguishable among the strains from other genomospecies of the genus Agrobacterium. Phylogenetic analyses of the 16S rRNA gene, gyrB gene, multi-locus sequence analysis, and 1,089-gene core-genome gene concatenate concur that tested G3 strains belong to the Agrobacterium genus and they form a clade distinct from other validly described Agrobacterium species. The distinctiveness of this clade was confirmed by average nucleotide identity (ANI) and in silico digital DNA-DNA hybridization (dDDH) comparisons between the G3 tested strains and all known Agrobacterium species type strains, since obtained values were considerably below the 95% (ANI) and 70% (dDDH) thresholds used for the species delineation. According to the core-genome phylogeny and ANI comparisons, the closest relatives of G3 strains were Agrobacterium sp. strains UGM030330-04 and K599, members of a novel genomospecies we propose to call genomovar G21. Using this polyphasic approach, we characterized the phenotypic and genotypic synapomorphies of Agrobacterium G3, showing it is a bona fide bacterial species, well separated from previously named Agrobacterium species or other recognized genomic species. We thus propose the name Agrobacterium tomkonis for this species previously referred to as Agrobacterium genomospecies 3. The type strain of A. tomkonis is IIF1SW-B1T (= LMG 32164 = NRRL B-65602). Comparative genomic analysis show A. tomkonis strains have species-specific genes associated with secretion of secondary metabolites, including an exopolysaccharide and putative adhesins and resistance to copper. A. tomkonis specific gene functions notably relate to surface adhesion and could be involved to colonize nutrient-poor and harsh habitats. The A. tomkonis strains from the ISS showed presence of a 40-kbp plasmid and several other potential mobile genetic elements detected that could also be part of conjugative elements or integrated prophages.}, }
@article {pmid34937787, year = {2021}, author = {Mirza, AI and Zhu, F and Knox, N and Forbes, JD and Van Domselaar, G and Bernstein, CN and Graham, M and Marrie, RA and Hart, J and Yeh, EA and Arnold, D and Bar-Or, A and O'Mahony, J and Zhao, Y and Hsiao, W and Banwell, B and Waubant, E and Tremlett, H}, title = {Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome.}, journal = {Neurology}, volume = {}, number = {}, pages = {}, doi = {10.1212/WNL.0000000000013245}, pmid = {34937787}, issn = {1526-632X}, abstract = {BACKGROUND AND OBJECTIVES: Little is known of the functional potential of the gut microbiome in pediatric-onset multiple sclerosis (MS). We performed metagenomic analyses using stool samples from individuals with pediatric-onset MS and unaffected controls.<br><br>METHODS: Persons ≤21 years old enrolled in the Canadian Pediatric Demyelinating Disease Network providing a stool sample were eligible. Twenty MS patients (McDonald criteria) with symptom onset <18 years were matched to 20 controls by sex, age (±3 years), stool consistency, and race. Microbial taxonomy and functional potentials were estimated from stool sample-derived metagenomic reads and compared by disease status (MS vs controls) and disease-modifying drug (DMD) exposure using alpha-diversity, relative abundance, and prevalence using Wilcoxon rank-sum, ALDEx2 and Fisher's exact tests, respectively.<br><br>RESULTS: Individuals with MS were aged 13.6 years (mean) at symptom onset and 8 were DMD naïve. Mean ages at stool sample were 16.1 and 15.4 years for MS and control participants, respectively; 80% were girls. Alpha-diversity of enzymes and proteins did not differ by disease or DMD status (p>0.20), but metabolic pathways, gene annotations and microbial taxonomy did. Individuals with MS (vs controls) exhibited higher methanogenesis prevalence (odds ratio=10, p=0.044), and Methanobrevibacter abundance (log2 fold-change[LFC]=1.7, p=0.0014), but lower homolactic fermentation abundance (LFC=-0.48, p=0.039). Differences by DMD status included lower phosphate butyryltransferase for DMD-naïve vs exposed MS patients (LFC=-1.0, p=0.033).<br><br>DISCUSSION: The gut microbiome's functional potential and taxonomy differed between individuals with pediatric-onset MS versus controls, including higher prevalence of a methane-producing pathway from Archaea and depletion of the lactate fermentation pathway. DMD exposure was associated with butyrate-producing enzyme enrichment. Together these findings indicate that the gut microbiome of individuals with MS may have a disturbed functional potential.}, }
@article {pmid34937766, year = {2021}, author = {Sugimura, N and Li, Q and Chu, ESH and Lau, HCH and Fong, W and Liu, W and Liang, C and Nakatsu, G and Su, ACY and Coker, OO and Wu, WKK and Chan, FKL and Yu, J}, title = {Lactobacillus gallinarum modulates the gut microbiota and produces anti-cancer metabolites to protect against colorectal tumourigenesis.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2020-323951}, pmid = {34937766}, issn = {1468-3288}, abstract = {OBJECTIVE: Using faecal shotgun metagenomic sequencing, we identified the depletion of Lactobacillus gallinarum in patients with colorectal cancer (CRC). We aimed to determine the potential antitumourigenic role of L. gallinarum in colorectal tumourigenesis.<br><br>DESIGN: The tumor-suppressive effect of L. gallinarum was assessed in murine models of CRC. CRC cell lines and organoids derived from patients with CRC were cultured with L. gallinarum or Escherichia coli MG1655 culture-supernatant to evaluate cell proliferation, apoptosis and cell cycle distribution. Gut microbiota was assessed by 16S ribosomal DNA sequencing. Antitumour molecule produced from L. gallinarum was identified by liquid chromatography mass spectrometry (LC-MS/MS) and targeted mass spectrometry.<br><br>RESULTS: L. gallinarum significantly reduced intestinal tumour number and size compared with E. coli MG1655 and phosphate-buffered saline in both male and female murine intestinal tumourigenesis models. Faecal microbial profiling revealed enrichment of probiotics and depletion of pathogenic bacteria in L. gallinarum-treated mice. Culturing CRC cells with L. gallinarum culture-supernatant (5%, 10% and 20%) concentration-dependently suppressed cell proliferation and colony formation. L. gallinarum culture-supernatant significantly promoted apoptosis in CRC cells and patient-derived CRC organoids, but not in normal colon epithelial cells. Only L. gallinarum culture-supernatant with fraction size <3 kDa suppressed proliferation in CRC cells. Using LC-MS/MS, enrichments of indole-3-lactic acid (ILA) was identified in both L. gallinarum culture-supernatant and the gut of L. gallinarum-treated mice. ILA displayed anti-CRC growth in vitro and inhibited intestinal tumourigenesis in vivo.<br><br>CONCLUSION: L. gallinarum protects against intestinal tumourigenesis by producing protective metabolites that can promote apoptosis of CRC cells.}, }
@article {pmid34936673, year = {2021}, author = {Voigt, B and Fischer, O and Krumnow, C and Herta, C and Dabrowski, PW}, title = {NGS read classification using AI.}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0261548}, doi = {10.1371/journal.pone.0261548}, pmid = {34936673}, issn = {1932-6203}, abstract = {Clinical metagenomics is a powerful diagnostic tool, as it offers an open view into all DNA in a patient's sample. This allows the detection of pathogens that would slip through the cracks of classical specific assays. However, due to this unspecific nature of metagenomic sequencing, a huge amount of unspecific data is generated during the sequencing itself and the diagnosis only takes place at the data analysis stage where relevant sequences are filtered out. Typically, this is done by comparison to reference databases. While this approach has been optimized over the past years and works well to detect pathogens that are represented in the used databases, a common challenge in analysing a metagenomic patient sample arises when no pathogen sequences are found: How to determine whether truly no evidence of a pathogen is present in the data or whether the pathogen's genome is simply absent from the database and the sequences in the dataset could thus not be classified? Here, we present a novel approach to this problem of detecting novel pathogens in metagenomic datasets by classifying the (segments of) proteins encoded by the sequences in the datasets. We train a neural network on the sequences of coding sequences, labeled by taxonomic domain, and use this neural network to predict the taxonomic classification of sequences that can not be classified by comparison to a reference database, thus facilitating the detection of potential novel pathogens.}, }
@article {pmid34936221, year = {2021}, author = {Manni, M and Berkeley, MR and Seppey, M and Zdobnov, EM}, title = {BUSCO: Assessing Genomic Data Quality and Beyond.}, journal = {Current protocols}, volume = {1}, number = {12}, pages = {e323}, doi = {10.1002/cpz1.323}, pmid = {34936221}, issn = {2691-1299}, support = {310030_189062//University of Geneva, Swiss National Science Foundation/ ; }, abstract = {Evaluation of the quality of genomic "data products" such as genome assemblies or gene sets is of critical importance in order to recognize possible issues and correct them during the generation of new data. It is equally essential to guide subsequent or comparative analyses with existing data, as the correct interpretation of the results necessarily requires knowledge about the quality level and reliability of the inputs. Using datasets of near universal single-copy orthologs derived from OrthoDB, BUSCO can estimate the completeness and redundancy of genomic data by providing biologically meaningful metrics based on expected gene content. These can complement technical metrics such as contiguity measures (e.g., number of contigs/scaffolds, and N50 values). Here, we describe the use of the BUSCO tool suite to assess different data types that can range from genome assemblies of single isolates and assembled transcriptomes and annotated gene sets to metagenome-assembled genomes where the taxonomic origin of the species is unknown. BUSCO is the only tool capable of assessing all these types of sequences from both eukaryotic and prokaryotic species. The protocols detail the various BUSCO running modes and the novel workflows introduced in versions 4 and 5, including the batch analysis on multiple inputs, the auto-lineage workflow to run assessments without specifying a dataset, and a workflow for the evaluation of (large) eukaryotic genomes. The protocols further cover the BUSCO setup, guidelines to interpret the results, and BUSCO "plugin" workflows for performing common operations in genomics using BUSCO results, such as building phylogenomic trees and visualizing syntenies. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Assessing an input sequence with a BUSCO dataset specified manually Basic Protocol 2: Assessing an input sequence with a dataset automatically selected by BUSCO Basic Protocol 3: Assessing multiple inputs Alternate Protocol: Decreasing analysis runtime when assessing a large number of small genomes with BUSCO auto-lineage workflow and Snakemake Support Protocol 1: BUSCO setup Support Protocol 2: Visualizing BUSCO results Support Protocol 3: Building phylogenomic trees.}, }
@article {pmid34936025, year = {2021}, author = {Vijayakumar, VR and Saravanan, K and Somasundaram, M and Jayaraj, R and Annamalai, P and Nooruddin, T and Dharumadurai, D}, title = {Metagenomic analysis of lichen-associated bacterial community profiling in Roccella montagnei.}, journal = {Archives of microbiology}, volume = {204}, number = {1}, pages = {54}, pmid = {34936025}, issn = {1432-072X}, abstract = {A lichen is a composite organism formed of algae or cyanobacteria that live in a mutually advantageous symbiotic relationship with the filaments (hyphae) of fungus. Three lichen samples were obtained from diverse sites at a terrestrial habitat located in Coimbatore and coastal habitats located in Kanyakumari and Nagapattinam districts of Tamil Nadu. Amplification and sequencing of 16S rRNA V3-V4 regions were used for metagenomic study. Aside from the Next-Generation Sequencing data (NGS), distinct types of lichen microbiome profiles were clearly revealed. The bacterial diversity in the lichen genera of Roccella montagnei growing in coastal and terrestrial environments was further investigated using common and unique operational taxonomic units (OTUs) and the QIIME pipeline (1.9.1). Using similarity clustering, the heat map analysis depicts the abundance information of chosen OTUs as well as the similarity and difference between OTUs and lichen samples. Using multiple methods, the alpha and beta diversity analysis revealed that there were differences in all of the samples. However, UPGMA tree inference of comparable bacterial community in coastal habitat lichen samples compared to terrestrial habitat validates their evolutionary lineage. As a result, the bacterial population associated with corticolous lichen is dependent on geographic locations, growth substrate, and climatic circumstances of similar lichen genera produced in different habitats and tree substrates.}, }
@article {pmid34935428, year = {2021}, author = {Zhang, RM and Sun, J and Sun, RY and Wang, MG and Cui, CY and Fang, LX and Liao, MN and Lu, XQ and Liu, YX and Liao, XP and Liu, YH}, title = {Source Tracking and Global Distribution of the Tigecycline Non-Susceptible tet(X).}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0116421}, doi = {10.1128/Spectrum.01164-21}, pmid = {34935428}, issn = {2165-0497}, abstract = {The emergence of tet(X) genes has compromised the clinical use of the last-line antibiotic tigecycline. We identified 322 (1.21%) tet(X) positive samples from 12,829 human microbiome samples distributed in four continents (Asia, Europe, North America, and South America) using retrospective data from worldwide. These tet(X) genes were dominated by tet(X2)-like orthologs but we also identified 12 samples carrying novel tet(X) genes, designed tet(X45), tet(X46), and tet(X47), were resistant to tigecycline. The metagenomic analysis indicated these tet(X) genes distributed in anaerobes dominated by Bacteroidaceae (78.89%) of human-gut origin. Two mobile elements ISBf11 and IS4351 were most likely to promote the transmission of these tet(X2)-like orthologs between Bacteroidaceae and Riemerella anatipestifer. tet(X2)-like orthologs was also developed during transmission by mutation to high-level tigecycline resistant genes tet(X45), tet(X46), and tet(X47). Further tracing these tet(X) in single bacterial isolate from public repository indicated tet(X) genes were present as early as 1960s in R. anatipestifer that was the primary tet(X) carrier at early stage (before 2000). The tet(X2) and non-tet(X2) orthologs were primarily distributed in humans and food animals respectively, and non-tet(X2) were dominated by tet(X3) and tet(X4). Genomic comparison indicated these tet(X) genes were likely to be generated during tet(X) transmission between Flavobacteriaceae and E. coli/Acinetobacter spp., and ISCR2 played a key role in the transmission. These results suggest R. anatipestifer was the potential ancestral source of tet(X). In addition, Bacteroidaceae of human-gut origin was an important hidden reservoir and mutational incubator for the mobile tet(X) genes that enabled spread to facultative anaerobes and aerobes. IMPORTANCE The emergence of the tigecycline resistance gene tet(X) has posed a severe threat to public health. However, reports of its origin and distribution in human remain rare. Here, we explore the origin and distribution of tet(X) from large-scale metagenomic data of human-gut origin and public repository. This study revealed the emergency of tet(X) gene in 1960s, which has refreshed a previous standpoint that the earliest presence of tet(X) was in 1980s. The metagenomic analysis from data mining covered the unculturable bacteria, which has overcome the traditional bacteria isolating and purificating technologies, and the analysis indicated that the Bacteroidaceae of human-gut origin was an important hidden reservoir for tet(X) that enabled spread to facultative anaerobes and aerobes. The continuous monitoring of mobile tigecycline resistance determinants from both culturable and unculturable microorganisms is imperative for understanding and tackling the dissemination of tet(X) genes in both the health care and agricultural sectors.}, }
@article {pmid34935421, year = {2021}, author = {Shen, S and Huo, D and Ma, C and Jiang, S and Zhang, J}, title = {Expanding the Colorectal Cancer Biomarkers Based on the Human Gut Phageome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0009021}, doi = {10.1128/Spectrum.00090-21}, pmid = {34935421}, issn = {2165-0497}, abstract = {With the increasing prevalence of colorectal cancer (CRC), extending the present biomarkers for the diagnosis of colorectal cancer is crucial. Previous studies have highlighted the importance of bacteriophages in gastrointestinal diseases, suggesting the potential value of gut phageome in early CRC diagnostic. Here, based on 317 metagenomic samples of three discovery cohorts collected from China (Hong Kong), Austria, and Japan, five intestinal bacteriophages, including Fusobacterium nucleatum, Peptacetobacter hiranonis, and Parvimonas micra phages were identified as potential CRC biomarkers. The five CRC enriched bacteriophagic markers classified patients from controls with an area under the receiver-operating characteristics curve (AUC) of 0.8616 across different populations. Subsequently, we used a total of 80 samples from China (Hainan) and Italy for validation. The AUC of the validation cohort is 0.8197. Moreover, to further explore the specificity of the five intestinal bacteriophage biomarkers in a broader background, we performed a confirmatory meta-analysis using two inflammatory bowel disease cohorts, ulcerative colitis (UC) and Crohn's disease (CD). Excitingly, we observed that the five CRC-enriched phage markers also exhibited high discrimination in UC (AUC = 78.02%). Unfortunately, the five CRC-rich phage markers did not show high resolution in CD (AUC = 48.00%). The present research expands the potential of microbial biomarkers in CRC diagnosis by building a more accurate classification model based on the human gut phageome, providing a new perspective for CRC gut phagotherapy. IMPORTANCE Worldwide, by 2020, colorectal cancer has become the third most common cancer after lung and breast cancer. Phages are strictly host-specific, and this specificity makes them more accurate as biomarkers, but phage biomarkers for colorectal cancer have not been thoroughly explored. Therefore, it is crucial to extend the existing phage biomarkers for the diagnosis of colorectal cancer. Here, we innovatively constructed a relatively accurate prediction model, including: three discovery cohorts, two additional validation cohorts and two cross-disease cohorts. A total of five possible biomarkers of intestinal bacteriophages were obtained. They are Peptacetobacter hiranonis Phage, Fusobacterium nucleatum animalis 7_1 Phage, Fusobacterium nucleatum polymorphum Phage, Fusobacterium nucleatum animalis 4_8 Phage, and Parvimonas micra Phage. This study aims at identifying fine-scale species-strain level phage biomarkers for colorectal cancer diseases, so as to expand the existing CRC biomarkers and provide a new perspective for intestinal phagocytosis therapy of colorectal cancer.}, }
@article {pmid34934888, year = {2021}, author = {Vrijheid, M and Basagaña, X and Gonzalez, JR and Jaddoe, VWV and Jensen, G and Keun, HC and McEachan, RRC and Porcel, J and Siroux, V and Swertz, MA and Thomsen, C and Aasvang, GM and Andrušaitytė, S and Angeli, K and Avraam, D and Ballester, F and Burton, P and Bustamante, M and Casas, M and Chatzi, L and Chevrier, C and Cingotti, N and Conti, D and Crépet, A and Dadvand, P and Duijts, L and van Enckevort, E and Esplugues, A and Fossati, S and Garlantezec, R and Gómez Roig, MD and Grazuleviciene, R and Gützkow, KB and Guxens, M and Haakma, S and Hessel, EVS and Hoyles, L and Hyde, E and Klanova, J and van Klaveren, JD and Kortenkamp, A and Le Brusquet, L and Leenen, I and Lertxundi, A and Lertxundi, N and Lionis, C and Llop, S and Lopez-Espinosa, MJ and Lyon-Caen, S and Maitre, L and Mason, D and Mathy, S and Mazarico, E and Nawrot, T and Nieuwenhuijsen, M and Ortiz, R and Pedersen, M and Perelló, J and Pérez-Cruz, M and Philippat, C and Piler, P and Pizzi, C and Quentin, J and Richiardi, L and Rodriguez, A and Roumeliotaki, T and Sabin Capote, JM and Santiago, L and Santos, S and Siskos, AP and Strandberg-Larsen, K and Stratakis, N and Sunyer, J and Tenenhaus, A and Vafeiadi, M and Wilson, RC and Wright, J and Yang, T and Slama, R}, title = {Advancing tools for human early lifecourse exposome research and translation (ATHLETE): Project overview.}, journal = {Environmental epidemiology (Philadelphia, Pa.)}, volume = {5}, number = {5}, pages = {e166}, pmid = {34934888}, issn = {2474-7882}, abstract = {Early life stages are vulnerable to environmental hazards and present important windows of opportunity for lifelong disease prevention. This makes early life a relevant starting point for exposome studies. The Advancing Tools for Human Early Lifecourse Exposome Research and Translation (ATHLETE) project aims to develop a toolbox of exposome tools and a Europe-wide exposome cohort that will be used to systematically quantify the effects of a wide range of community- and individual-level environmental risk factors on mental, cardiometabolic, and respiratory health outcomes and associated biological pathways, longitudinally from early pregnancy through to adolescence. Exposome tool and data development include as follows: (1) a findable, accessible, interoperable, reusable (FAIR) data infrastructure for early life exposome cohort data, including 16 prospective birth cohorts in 11 European countries; (2) targeted and nontargeted approaches to measure a wide range of environmental exposures (urban, chemical, physical, behavioral, social); (3) advanced statistical and toxicological strategies to analyze complex multidimensional exposome data; (4) estimation of associations between the exposome and early organ development, health trajectories, and biological (metagenomic, metabolomic, epigenetic, aging, and stress) pathways; (5) intervention strategies to improve early life urban and chemical exposomes, co-produced with local communities; and (6) child health impacts and associated costs related to the exposome. Data, tools, and results will be assembled in an openly accessible toolbox, which will provide great opportunities for researchers, policymakers, and other stakeholders, beyond the duration of the project. ATHLETE's results will help to better understand and prevent health damage from environmental exposures and their mixtures from the earliest parts of the life course onward.}, }
@article {pmid34934772, year = {2021}, author = {Davar, K and Wilson, MR and Miller, S and Chiu, CY and Vijayan, T}, title = {A Rare Bird: Diagnosis of Psittacosis Meningitis by Clinical Metagenomic Next-Generation Sequencing.}, journal = {Open forum infectious diseases}, volume = {8}, number = {12}, pages = {ofab555}, pmid = {34934772}, issn = {2328-8957}, abstract = {Psittacosis is a zoonotic infectious disease caused by the transmission of Chlamydia psittaci; it often presents as a pulmonary infection but rarely as disseminated disease. Because diagnoses of psittacosis are often underreported due to infrequent pathogen-specific testing, clinical metagenomic next-generation sequencing may be helpful to diagnose such an uncommon syndrome.}, }
@article {pmid34253055, year = {2021}, author = {Jaffe, AL and Thomas, AD and He, C and Keren, R and Valentin-Alvarado, LE and Munk, P and Bouma-Gregson, K and Farag, IF and Amano, Y and Sachdeva, R and West, PT and Banfield, JF}, title = {Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria.}, journal = {mBio}, volume = {12}, number = {4}, pages = {e0052121}, pmid = {34253055}, issn = {2150-7511}, mesh = {Animals ; Bacteria/*classification/*genetics ; Ecosystem ; *Evolution, Molecular ; Genome, Bacterial ; Genomics ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Candidate Phyla Radiation (CPR) bacteria are small, likely episymbiotic organisms found across Earth's ecosystems. Despite their prevalence, the distribution of CPR lineages across habitats and the genomic signatures of transitions among these habitats remain unclear. Here, we expand the genome inventory for Absconditabacteria (SR1), Gracilibacteria, and Saccharibacteria (TM7), CPR bacteria known to occur in both animal-associated and environmental microbiomes, and investigate variation in gene content with habitat of origin. By overlaying phylogeny with habitat information, we show that bacteria from these three lineages have undergone multiple transitions from environmental habitats into animal microbiomes. Based on co-occurrence analyses of hundreds of metagenomes, we extend the prior suggestion that certain Saccharibacteria have broad bacterial host ranges and constrain possible host relationships for Absconditabacteria and Gracilibacteria. Full-proteome analyses show that animal-associated Saccharibacteria have smaller gene repertoires than their environmental counterparts and are enriched in numerous protein families, including those likely functioning in amino acid metabolism, phage defense, and detoxification of peroxide. In contrast, some freshwater Saccharibacteria encode a putative rhodopsin. For protein families exhibiting the clearest patterns of differential habitat distribution, we compared protein and species phylogenies to estimate the incidence of lateral gene transfer and genomic loss occurring over the species tree. These analyses suggest that habitat transitions were likely not accompanied by large transfer or loss events but rather were associated with continuous proteome remodeling. Thus, we speculate that CPR habitat transitions were driven largely by availability of suitable host taxa and were reinforced by acquisition and loss of some capacities. IMPORTANCE Studying the genetic differences between related microorganisms from different environment types can indicate factors associated with their movement among habitats. This is particularly interesting for bacteria from the Candidate Phyla Radiation because their minimal metabolic capabilities require associations with microbial hosts. We found that shifts of Absconditabacteria, Gracilibacteria, and Saccharibacteria between environmental ecosystems and mammalian mouths/guts probably did not involve major episodes of gene gain and loss; rather, gradual genomic change likely followed habitat migration. The results inform our understanding of how little-known microorganisms establish in the human microbiota where they may ultimately impact health.}, }
@article {pmid33860293, year = {2021}, author = {Ding, J and Ma, X and Han, L and Zhao, X and Li, A and Xin, Q and Lian, W and Li, Z and Ren, H and Ren, Z}, title = {Gut microbial alterations in neonatal jaundice pre- and post-treatment.}, journal = {Bioscience reports}, volume = {41}, number = {4}, pages = {}, pmid = {33860293}, issn = {1573-4935}, mesh = {Drugs, Chinese Herbal/pharmacology/therapeutic use ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Infant, Newborn ; Jaundice, Neonatal/drug therapy/*microbiology ; Male ; Metagenome ; }, abstract = {Neonatal jaundice is a common disease that affects up to 60% of newborns. Herein, we performed a comparative analysis of the gut microbiome in neonatal jaundice and non-neonatal jaundice infants (NJIs) and identified gut microbial alterations in neonatal jaundice pre- and post-treatment. We prospectively collected 232 fecal samples from 51 infants at five time points (0, 1, 3, 6, and 12 months). Finally, 114 samples from 6 NJIs and 19 non-NJI completed MiSeq sequencing and analysis. We characterized the gut microbiome and identified microbial differences and gene functions. Meconium microbial diversity from NJI was decreased compared with that from non-NJI. The genus Gemella was decreased in NJI versus non-NJI. Eleven predicted microbial functions, including fructose 1,6-bisphosphatase III and pyruvate carboxylase subunit B, decreased, while three functions, including acetyl-CoA acyltransferase, increased in NJI. After treatments, the microbial community presented significant alteration-based β diversity. The phyla Firmicutes and Actinobacteria were increased, while Proteobacteria and Fusobacteria were decreased. Microbial alterations were also analyzed between 6 recovered NJI and 19 non-NJI. The gut microbiota was unique in the meconium microbiome from NJI, implying that early gut microbiome intervention could be promising for the management of neonatal jaundice. Alterations of gut microbiota from NJI can be of great value to bolster evidence-based prevention against 'bacterial dysbiosis'.}, }
@article {pmid34933230, year = {2021}, author = {Santiago, LD and DeLeon-Rodriguez, N and LaSanta-Pagán, K and Hatt, JK and Kurt, Z and Massol-Deyá, A and Konstantinidis, KT}, title = {Microbial diversity in a military impacted lagoon (Vieques, Puerto Rico) and description of "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. comprising a new bacterial family.}, journal = {Systematic and applied microbiology}, volume = {45}, number = {1}, pages = {126288}, doi = {10.1016/j.syapm.2021.126288}, pmid = {34933230}, issn = {1618-0984}, abstract = {The Anones Lagoon, located in the Island Municipality of Vieques, Puerto Rico (PR), received extensive bombing by the US Navy during military exercises for decades until 2003 when military activities ceased. Here, we employed shotgun metagenomic sequencing to investigate how microbial communities responded to pollution by heavy metals and explosives at this lagoon. Sediment samples (0-5 cm) from Anones were collected in 2005 and 2014 and compared to samples from two reference lagoons, i.e., Guaniquilla, Cabo Rojo (a natural reserve) and Condado, San Juan (PR's capital city). Consistent with low anthropogenic inputs, Guaniquilla exhibited the highest degree of diversity with a lower frequency of genes related to xenobiotics metabolism between the three lagoons. Notably, a clear shift was observed in Anones, with Euryarchaeota becoming enriched (9% of total) and a concomitant increase in community diversity, by about one order of magnitude, after almost 10 years without bombing activities. In contrast, genes associated with explosives biodegradation and heavy metal transformation significantly decreased in abundance in Anones 2014 (by 91.5%). Five unique metagenome-assembled genomes (MAGs) were recovered from the Anones 2005 sample that encoded genetic determinants implicated in biodegradation of contaminants, and we propose to name one of them as "Candidatus Biekeibacterium resiliens" gen. nov., sp. nov. within the Gammaproteobacteria class. Collectively, these results provide new insights into the natural attenuation of explosive contaminants by the benthic microbial communities of the Anones lagoon and provide a reference point for assessing other similarly impacted sites and associated bioremediation efforts.}, }
@article {pmid34932985, year = {2021}, author = {Kim, AH and Armah, G and Dennis, F and Wang, L and Rodgers, R and Droit, L and Baldridge, MT and Handley, SA and Harris, VC}, title = {Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2021.12.002}, pmid = {34932985}, issn = {1934-6069}, abstract = {Rotavirus vaccines (RVVs) have substantially diminished mortality from severe rotavirus (RV) gastroenteritis but are significantly less effective in low- and middle-income countries (LMICs), limiting their life-saving potential. The etiology of RVV's diminished effectiveness remains incompletely understood, but the enteric microbiota has been implicated in modulating immunity to RVVs. Here, we analyze the enteric microbiota in a longitudinal cohort of 122 Ghanaian infants, evaluated over the course of 3 Rotarix vaccinations between 6 and 15 weeks of age, to assess whether bacterial and viral populations are distinct between non-seroconverted and seroconverted infants. We identify bacterial taxa including Streptococcus and a poorly classified taxon in Enterobacteriaceae as positively correlating with seroconversion. In contrast, both bacteriophage diversity and detection of Enterovirus B and multiple novel cosaviruses are negatively associated with RVV seroconversion. These findings suggest that virome-RVV interference is an underappreciated cause of poor vaccine performance in LMICs.}, }
@article {pmid34931899, year = {2021}, author = {Terensan, S and Fernando, N and Perera, C and Silva, N and Kottearachchi, N and Weerasena, OVDSJ}, title = {Morphological and Molecular Analysis of Fungal Species Associated with Blast and Brown Spot Diseases of Oryzae sativa.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-04-21-0864-RE}, pmid = {34931899}, issn = {0191-2917}, abstract = {Fungal diseases; blast, and brown spot in rice incur severe yield losses worldwide. Blast is caused by Magnaporthe oryzae, while Bipolaris oryzae is reported as the main causal organism of brown spot. Both diseases cause leaf lesions which are difficult to be differentiated by symptomatology until the late stages. Early detection and differentiation of the lesions would help the adoption of disease management strategies specific to the pathogen and will prevent the native impact on the quality and quantity of rice yields. This study was conducted in the Northern Province of Sri Lanka over five consecutive rice cultivating seasons to characterize the causal fungi of rice blast and brown spot diseases by morphological and molecular means and to develop a visual guide to differentiate the two diseases. Disease incidence was recorded in 114 fields from 2017 to 2019, and fungal isolates associated with lesions of both the diseases were cultured and subjected to morphological and molecular characterization. Competitive growth interaction between M. oryzae and the more common individual fungal isolates of the brown spot lesions, was evaluated. Fungal metagenomics analysis was conducted for the fungal spp. isolated from brown spot lesions. A suppression of blast accompanied by an increased incidence of brown spot disease was observed during the study period. M. oryzae was confirmed to be the causal organism of the blast while over 20 species of fungi were identified to be associated with brown spot lesions through morphological, molecular studies, and metagenomics analyses. Fungal ITS region sequencing revealed considerable genetic variation in the highly conserved region of DNA sequences of blast and brown spot fungal isolates. B. oryzae, Curvularia, and Microdochium species were commonly isolated from brown spot lesions. In vitro competitive growth interaction among the fungal isolates revealed growth suppression of M. oryzae by the fungal isolates associated with the brown spot lesions. Similarly, it can be speculated that the abundance and severity of blast in the field may have an influence on brown spot associated fungi. A simple visual guide was developed to differentiate blast and brown spot lesions. The findings would be highly useful in the timely management of these major fungal diseases affecting rice.}, }
@article {pmid34931883, year = {2021}, author = {Der Sarkissian, C and Velsko, IM and Fotakis, AK and Vågene, ÅJ and Hübner, A and Fellows Yates, JA}, title = {Ancient Metagenomic Studies: Considerations for the Wider Scientific Community.}, journal = {mSystems}, volume = {6}, number = {6}, pages = {e0131521}, doi = {10.1128/msystems.01315-21}, pmid = {34931883}, issn = {2379-5077}, support = {Paleobiotechnology//Werner Siemens-Stiftung/ ; CEH - DNRF143//Danmarks Grundforskningsfond (DNRF)/ ; CF18-1109//Carlsbergfondet (Carlsberg Foundation)/ ; //Centre National de la Recherche Scientifique (CNRS)/ ; 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; ERC-2015-StG 678901-FoodTransforms//EC | H2020 | H2020 Priority Excellent Science | H2020 European Research Council (ERC)/ ; //Max-Planck-Gesellschaft (MPG)/ ; }, abstract = {Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions &amp; Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.}, }
@article {pmid34931478, year = {2021}, author = {Mashiah, J and Karady, T and Fliss-Isakov, N and Sprecher, E and Slodownik, D and Artzi, O and Samuelov, L and Ellenbogen, E and Godneva, A and Segal, E and Maharshak, N}, title = {Clinical efficacy of fecal microbial transplantation treatment in adults with moderate-to-severe atopic dermatitis.}, journal = {Immunity, inflammation and disease}, volume = {}, number = {}, pages = {}, doi = {10.1002/iid3.570}, pmid = {34931478}, issn = {2050-4527}, abstract = {BACKGROUND: Atopic dermatitis (AD) is a remitting relapsing chronic eczematous pruritic disease. Several studies suggest that gut microbiota may influence AD by immune system regulation.<br><br>METHODS: We performed the first in-human efficacy and safety assessment of fecal microbiota transplantation (FMT) for AD adult patients. All patients received 2 placebo transplantations followed by 4 FMTs each 2 weeks apart. AD severity and fecal microbiome profile were evaluated by the Scoring Atopic Dermatitis Score (SCORAD), the weekly frequency of topical corticosteroids usage, and gut microbiota metagenomic analysis, at the study beginning, before every FMT, and 1-8 months after the last FMT.<br><br>RESULTS: Nine patients completed the study protocol. There was no significant change in the SCORAD score following the two placebo transplants. The average SCORAD score significantly decreased from baseline at Weeks 4-12 (before and 2 weeks after 4 times of FMT) (59.2 ± 34.9%, Wilcoxon p = .011), 50% and 75% decrease was achieved by 7 (77%) and 4 (44%) patients, respectively. At Week 18 (8 weeks after the last FMT) the average SCORAD score decreased from baseline at Week 4 (85.5 ± 8.4%, Wilcoxon p = .018), 50% and 75% decrease was achieved by 7 (77%) and 6 (66.7%) patients respectively. Weekly topical corticosteroids usage was diminished during the study and follow-up period as well. Two patients had a quick relapse and were switched to a different treatment. Two patients developed exacerbations alleviated after an additional fifth FMT. Metagenomic analysis of the fecal microbiota of patients and donors showed bacterial strains transmission from donors to patients. No adverse events were recorded during the study and follow-up period.<br><br>CONCLUSIONS: FMT may be a safe and effective therapeutic intervention for AD patients, associated with transfer of specific microbial species from the donors to the patients. Further studies are required to reconfirm these results.}, }
@article {pmid34930990, year = {2021}, author = {Liu, H and Qi, Y and Wang, J and Jiang, Y and Geng, M}, title = {Synergistic effects of crop residue and microbial inoculant on soil properties and soil disease resistance in a Chinese Mollisol.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {24225}, pmid = {34930990}, issn = {2045-2322}, support = {41877027//National Natural Science Foundation of China/ ; 20200402002NC//Major Science and Technology Projects in Jilin Province/ ; }, abstract = {The soil-borne disease caused by Fusarium graminearum seriously affects the corn quality. Straw can greatly improve soil quality, but the effect is limited by its nature and environmental factors. This study explored the impact of straw-JF-1(biocontrol bacteria) combination on soil environment and soil disease resistance. The results showed that the combined treatment increased the proportion of soil large and small macro-aggregates by 22.50 and 3.84%, with soil organic carbon (SOC) content by 16.18 and 16.95%, respectively. Compared to treatment with returning straw to the field alone, the straw-JF-1 combination increased the soil content of humic acid, fulvic acid, and humin by 14.06, 5.50, and 4.37%, respectively. Moreover, A metagenomics showed that returning straw to the field alone increased the abundance of disease-causing fungi (Fusarium and Plectosphaerella), however, the straw-JF-1 combination significantly suppressed this phenomenon as well as improved the abundance of probiotic microorganisms such as Sphingomonas, Mortierella, Bacillus, and Pseudomonas. Functional analysis indicated that the combination of straw and JF-1 improved some bacterial functions, including inorganic ion transport and metabolism, post-translational modification/protein turnover/chaperones and function unknown, fungal functions associated with plant and animal pathogens were effectively inhibited. Pot experiments showed that the straw-JF-1 combination effectively inhibited the Fusarium graminearum induced damage to maize seedlings. Therefore, the combination of straw and JF-1 could be a practical method for soil management.}, }
@article {pmid34930479, year = {2021}, author = {Leonard, SR and Simko, I and Mammel, MK and Richter, TKS and Brandl, MT}, title = {Seasonality, shelf life and storage atmosphere are main drivers of the microbiome and E. coli O157:H7 colonization of post-harvest lettuce cultivated in a major production area in California.}, journal = {Environmental microbiome}, volume = {16}, number = {1}, pages = {25}, pmid = {34930479}, issn = {2524-6372}, support = {2030-42000-052-00-D//agricultural research service/ ; 2038-21530-002-00-D//agricultural research service/ ; }, abstract = {BACKGROUND: Lettuce is linked to recurrent outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections, the seasonality of which remains unresolved. Infections have occurred largely from processed lettuce, which undergoes substantial physiological changes during storage. We investigated the microbiome and STEC O157:H7 (EcO157) colonization of fresh-cut lettuce of two cultivars with long and short shelf life harvested in the spring and fall in California and stored in modified atmosphere packaging (MAP) at cold and warm temperatures.<br><br>RESULTS: Inoculated EcO157 declined significantly less on the cold-stored cultivar with short shelf life, while multiplying rapidly at 24 °C independently of cultivar. Metagenomic sequencing of the lettuce microbiome revealed that the pre-storage bacterial community was variable but dominated by species in the Erwiniaceae and Pseudomonadaceae. After cold storage, the microbiome composition differed between cultivars, with a greater relative abundance (RA) of Erwiniaceae and Yersiniaceae on the cultivar with short shelf life. Storage at 24 °C shifted the microbiome to higher RAs of Erwiniaceae and Enterobacteriaceae and lower RA of Pseudomonadaceae compared with 6 °C. Fall harvest followed by lettuce deterioration were identified by recursive partitioning as important factors associated with high EcO157 survival at 6 °C, whereas elevated package CO2 levels correlated with high EcO157 multiplication at 24 °C. EcO157 population change correlated with the lettuce microbiome during 6 °C storage, with fall microbiomes supporting the greatest EcO157 survival on both cultivars. Fall and spring microbiomes differed before and during storage at both temperatures. High representation of Pantoea agglomerans was a predictor of fall microbiomes, lettuce deterioration, and enhanced EcO157 survival at 6 °C. In contrast, higher RAs of Erwinia persicina, Rahnella aquatilis, and Serratia liquefaciens were biomarkers of spring microbiomes and lower EcO157 survival.<br><br>CONCLUSIONS: The microbiome of processed MAP lettuce evolves extensively during storage. Under temperature abuse, high CO2 promotes a lettuce microbiome enriched in taxa with anaerobic capability and EcO157 multiplication. In cold storage, our results strongly support a role for season and lettuce deterioration in EcO157 survival and microbiome composition, suggesting that the physiology and microbiomes of fall- and spring-harvested lettuce may contribute to the seasonality of STEC outbreaks associated with lettuce grown in coastal California.}, }
@article {pmid34930331, year = {2021}, author = {Ning, SY and Zhou, MM and Yang, J and Zeng, J and Wang, JP}, title = {Viral metagenomics reveals two novel anelloviruses in feces of experimental rats.}, journal = {Virology journal}, volume = {18}, number = {1}, pages = {252}, pmid = {34930331}, issn = {1743-422X}, support = {BE2018040//the key R &amp; D projects of Jiangsu Province - industrial prospect and common key technology projects/ ; 1701043C//Postdoctoral Science Foundation of Jiangsu Province/ ; SWYY-194//Six Talent Peaks Project in Jiangsu Province/ ; }, abstract = {BACKGROUND: Rodents are widely distributed and are the natural reservoirs of a diverse group of zoonotic viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. Rodents are commonly used in animal testing, particularly mice and rats. Experimental rats are important animal models, and a history of pathogenic infections in these animals will directly affect the animal trial results. The pathogenicity of Anellovirus (AV) remains poorly understood due to the lack of a suitable model cell line or animal to support the viral cycle. This study aimed to discover possible anelloviruses from the virome in feces of experimental rats by viral metagenomic technique.<br><br>METHODS: Fecal samples were collected from 10 commercial SD rats and pooled into a sample pool and then subjected to libraries construction which was then sequenced on Illumina MiSeq platform. The sequenced reads were analyzed using viral metagenomic analysis pipeline and two novel anelloviruses (AVs) were identified from fecal sample of experimental rats. The prevalence of these two viruses was investigated by conventional PCR.<br><br>RESULTS: The complete genomic sequence of these two AVs were determined and fully characterized, with strain name ratane153-zj1 and ratane153-zj2. The circular genomes of ratane153-zj1 and ratane153-zj2 are 2785 nt and 1930 nt in length, respectively, and both include three ORFs. Ratane153-zj1 closely clustered with members within the genus Wawtorquevirus and formed a separate branch based on the phylogenetic tree constructed over the amino acid sequence of ORF1 of the two AVs identified in this study and other related AVs. While the complete amino acid sequences of ORF1 of ratane153-zj2 (nt 335 to 1390) had the highest sequence identity with an unclassified AV (GenBank No. ATY37438) from Chinchilla lanigera, and they clustered with one AV (GenBank No. QYD02305) belonging to the genus Etatorquevirus from Lynx rufus. Conventional PCR with two sets of specific primers designed based on the two genomes, respectively, showed that they were detectable at a low frequency in cohorts of experimental rats.<br><br>CONCLUSION: Our study expanded the genome diversity of AVs and provided genetic background information of viruses existed in experimental rats.}, }
@article {pmid34930148, year = {2021}, author = {Xing, N and Zhao, Z and Li, Q and Dong, Y and Li, J and Zhang, S}, title = {Ureaplasma parvum meningitis following atypical choroid plexus papilloma resection in an adult patient: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {21}, number = {1}, pages = {1276}, pmid = {34930148}, issn = {1471-2334}, abstract = {BACKGROUND: While Ureaplasma parvum has previously been linked to the incidence of chorioamnionitis, abortion, premature birth, and perinatal complications, there have only been rare reports of invasive infections of the central nervous system (CNS) in adults. Owing to its atypical presentation and the fact that it will yield sterile cultures using conventional techniques, diagnosing U. parvum meningitis can be challenging.<br><br>CASE PRESENTATION: We describe a case of U. parvum meningitis detected in an adult patient following surgical brain tumor ablation. After operation, the patient experienced epilepsy, meningeal irritation, and fever with unconsciousness. Cerebrospinal fluid (CSF) analysis showed leukocytosis (484 * 106 /L), elevated protein levels (1.92 g/L), and decreased glucose concentrations (0.02 mmol/L). Evidence suggested that the patient was suffering from bacterial meningitis. However, no bacterial pathogens in either CSF or blood were detected by routine culture or serology. The symptoms did not improve with empirical antibiotics. Therefore, we performed metagenomic next-generation sequencing (mNGS) to identify the etiology of the meningitis. Ureaplasma parvum was detected by mNGS in CSF samples. To the best of our knowledge, this case is the first reported instance of U. parvum meningitis in an adult patient in Asian. After diagnosis, the patient underwent successful moxifloxacin treatment and recovered without complications.<br><br>CONCLUSIONS: As mNGS strategies can enable the simultaneous detection of a diverse array of microbes in a single analysis, they may represent a valuable means of diagnosing the pathogens responsible for CNS infections and other clinical conditions with atypical presentations.}, }
@article {pmid34922440, year = {2021}, author = {Wahyudi, F and Aghakhanian, F and Rahman, S and Teo, YY and Szpak, M and Dhaliwal, J and Ayub, Q}, title = {Prioritising positively selected variants in whole-genome sequencing data using FineMAV.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {604}, pmid = {34922440}, issn = {1471-2105}, support = {Monash Graduate Research Scholarship//Monash University Malaysia/ ; }, mesh = {Blacks ; China ; *Genomics ; Humans ; *Metagenomics ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: In population genomics, polymorphisms that are highly differentiated between geographically separated populations are often suggestive of Darwinian positive selection. Genomic scans have highlighted several such regions in African and non-African populations, but only a handful of these have functional data that clearly associates candidate variations driving the selection process. Fine-Mapping of Adaptive Variation (FineMAV) was developed to address this in a high-throughput manner using population based whole-genome sequences generated by the 1000 Genomes Project. It pinpoints positively selected genetic variants in sequencing data by prioritizing high frequency, population-specific and functional derived alleles.<br><br>RESULTS: We developed a stand-alone software that implements the FineMAV statistic. To graphically visualise the FineMAV scores, it outputs the statistics as bigWig files, which is a common file format supported by many genome browsers. It is available as a command-line and graphical user interface. The software was tested by replicating the FineMAV scores obtained using 1000 Genomes Project African, European, East and South Asian populations and subsequently applied to whole-genome sequencing datasets from Singapore and China to highlight population specific variants that can be subsequently modelled. The software tool is publicly available at https://github.com/fadilla-wahyudi/finemav .<br><br>CONCLUSIONS: The software tool described here determines genome-wide FineMAV scores, using low or high-coverage whole-genome sequencing datasets, that can be used to prioritize a list of population specific, highly differentiated candidate variants for in vitro or in vivo functional screens. The tool displays these scores on the human genome browsers for easy visualisation, annotation and comparison between different genomic regions in worldwide human populations.}, }
@article {pmid33989546, year = {2021}, author = {Qiu, X and Hanage, WP and Taylor, BP}, title = {Coming to America: Genomic surveillance and how B.1.1.7 arrived in the US.}, journal = {Cell}, volume = {184}, number = {10}, pages = {2532-2534}, doi = {10.1016/j.cell.2021.04.031}, pmid = {33989546}, issn = {1097-4172}, mesh = {COVID-19/*epidemiology/virology ; Communicable Diseases, Emerging/*epidemiology/virology ; *Epidemiological Monitoring ; Humans ; Metagenomics/*methods ; SARS-CoV-2/genetics/*isolation &amp; purification ; United States/epidemiology ; }, abstract = {In this issue of Cell, Washington et al. and Alpert et al. demonstrate the value of genomic surveillance when studying the introduction of the B.1.1.7 variant to the US and illustrate the challenge that results from the lack of good sampling strategies.}, }
@article {pmid34929357, year = {2021}, author = {Guo, F and Kang, L and Zhang, L}, title = {mNGS for identifying pathogens in febrile neutropenic children with hematological diseases.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijid.2021.12.335}, pmid = {34929357}, issn = {1878-3511}, abstract = {OBJECTIVE: To investigate the application value of metagenomic next-generation sequencing (mNGS) in children with hematological diseases presenting with Febrile Neutropenic (FN).<br><br>METHODS: We retrospectively analyzed the clinical data of 49 hematological children with FN, and compared the results of mNGS with those of traditional pathogen detection (TPD) and the prognoses of mNGS positive group and negative group.<br><br>RESULTS: A total of 77 pathogenic strains were identified, of which 70 strains were detected by mNGS, 19 strains by TPD , and Aspergillus and G- bacterias were the predominant strains in FN children who developed bloodstream infections. 42 cases were in the mNGS-positive group, of which 17 were simple infections, 25 were mixed infections, and 7 were in the negative group; the TPD-positive group contained 19 cases, all of which were simple infections. The detection rate of total and mixed pathogens was higher than that of TPD, and the difference was statistically significant (P<0.05). mNGS positive group was detected earlier than the negative group, and with lower mortality and drug-related adverse events (DRAE) , and the difference was statistically significant (P<0.05).<br><br>CONCLUSION: For FN children with hematological diseases, early mNGS can effectively improve the efficacy of pathogen detection, and precise treatment after clarifying the pathogens can reduce mortality and avoid antibiotic abuse.}, }
@article {pmid34929178, year = {2021}, author = {David, EDS and Fonseca, EDC and de Carvalho, JFN and Marinho, RDSS and Duro, RLS and Komninakis, SV and Souto, RNP}, title = {Metagenomics applied to the detection of diarrhea viruses in humans: Systematic Review.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {106287}, doi = {10.1016/j.actatropica.2021.106287}, pmid = {34929178}, issn = {1873-6254}, abstract = {To analyze the application of the metagenomics method in the identification of viral infectious agents that lead to diarrhea outbreaks. This study is a systematic review, which looked for publications on the following platforms: PubMed, Scientific Electronic Library 2Online (SciELO), LILACS and CAPES periodicals, conducted according to the PRISMA methodology, investigating in the literary composition studies related to metagenomics applied in the identification of viral infectious agents, which lead to diarrhea in humans. 1198 publications were identified. Of these, after analyzes and exclusions at different stages, 18 studies remained, which directly corresponded to the theme. Diarrhea was presented as a universal health concern. Despite the emergence of vaccines, cases of diarrhea remain persistent in poor populations. In this context, metagenomics emerges as a primary tool in detecting enteric viruses and identifying new viruses, revolutionizing health diagnoses, knowledge of viral diversity, and health surveillance, contributing to the correct etiology of infectious agents that would never be identified by conventional methods. The 18 articles studied point to advances in research in viral metagenomics of diarrheal samples, contributing to the discernment of diarrhea outbreaks, and properly associating with their etiological agents, they are presented in an innovative way for studies on the understanding of viral diversity.}, }
@article {pmid34928868, year = {2021}, author = {Nobel, YR and Rozenberg, F and Park, H and Freedberg, DE and Blaser, MJ and Green, PHR and Uhlemann, AC and Lebwohl, B}, title = {Lack of Effect of Gluten Challenge on Fecal Microbiome in Patients With Celiac Disease and Non-Celiac Gluten Sensitivity.}, journal = {Clinical and translational gastroenterology}, volume = {12}, number = {12}, pages = {e00441}, doi = {10.14309/ctg.0000000000000441}, pmid = {34928868}, issn = {2155-384X}, abstract = {INTRODUCTION: Celiac disease (CD) may be associated with gut microbial dysbiosis. Whether discrete gluten exposure in subjects with well-controlled disease on a gluten-free diet impacts the gut microbiome is unknown and may have implications for understanding disease activity and symptoms. We conducted a prospective study to evaluate the impact of gluten exposure on the gut microbiome in patients with CD and nonceliac gluten sensitivity (NCGS).<br><br>METHODS: Subjects with CD (n = 9) and NCGS (n = 8) previously on a gluten-free diet were administered a 14-day gluten challenge (5 g of gluten per day) and compared with controls (n = 8) on a usual gluten-containing diet. Stool was collected for fecal microbiome analysis using 16S rRNA gene and metagenomic sequencing before, during, and after the gluten challenge. Symptoms were assessed using 2 validated clinical scales.<br><br>RESULTS: Among subjects with CD and NCGS, there were no significant fecal microbial changes in response to gluten challenge. Gut microbiome composition differed among controls, subjects with CD, and subjects with NCGS at baseline, and these differences persisted despite gluten exposure. Gastrointestinal and general health symptoms reported by subjects with CD and NCGS were worst in the middle of gluten challenge and lessened by its end, with no consistent associations with gut microbiome composition.<br><br>DISCUSSION: Pre-existing fecal microbiome diversity was unaffected by gluten challenge in adult subjects with CD and NCGS. These findings suggest that current microbiome status is unrelated to current disease activity and disease severity.}, }
@article {pmid34928204, year = {2021}, author = {Tochetto, C and Cibulski, SP and Muterle Varela, AP and Cerva, C and Alves de Lima, D and Fumaco Teixeira, T and Quoos Mayer, F and Roehe, PM}, title = {A variety of highly divergent eukaryotic ssDNA viruses in sera of pigs.}, journal = {The Journal of general virology}, volume = {102}, number = {12}, pages = {}, doi = {10.1099/jgv.0.001706}, pmid = {34928204}, issn = {1465-2099}, abstract = {Over the last decade, viral metagenomics has been established as a non-targeted approach for identifying viruses in stock animals, including pigs. This has led to the identification of a vast diversity of small circular ssDNA viruses. The present study focuses on the investigation of eukaryotic circular Rep-encoding single-stranded (CRESS) DNA viral genomes present in serum of commercially reared pigs from southern Brazil. Several CRESS DNA viral genomes were detected, including representatives of the families Smacoviridae (n=5), Genomoviridae (n=3), Redondoviridae (n=1), Nenyaviridae (n=1) and other yet unclassified genomes (n=9), plus a circular DNA molecule, which probably belongs to the phylum Cressdnaviricota. A novel genus within the family Smacoviridae, tentatively named 'Suismacovirus', comprising 21 potential new species, is proposed. Although the reported genomes were recovered from pigs with clinical signs of respiratory disease, further studies should examine their potential role as pathogens. Nonetheless, these findings highlight the diversity of circular ssDNA viruses in serum of domestic pigs, expand the knowledge on CRESS DNA viruses' genetic diversity and distribution and contribute to the global picture of the virome of commercially reared pigs.}, }
@article {pmid34927369, year = {2021}, author = {Ma, J and Yuan, Y and Shao, J and Sun, M and He, W and Chen, J and Liu, Q}, title = {Genomic characterization of lumpy skin disease virus in southern China.}, journal = {Transboundary and emerging diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/tbed.14432}, pmid = {34927369}, issn = {1865-1682}, abstract = {Lumpy skin disease virus (LSDV) is of high economic importance and has spread rapidly to many European and Asian countries in recent years. LSDVs was introduced to China in 2019 and have caused severe outbreaks in several provinces. Here, we detected a LSDV strain (GD01/2020) from a cattle farm with typical LSD symptoms in Guangdong, southern China using a novel quantitative real-time PCR assay targeting the viral GPCR gene. We obtained the whole genomic sequence of GD01/2020 through metagenomic analysis. The GD01/2020 was highly homologous to the LSDVs isolated in Xinjiang, China in 2019, and distinct from all the LSDVs identified in other countries, in their sequences of GPCR and RPO30 genes. The GD01/2020 was a vaccine-recombinant strain, but distinct from two recombinant LSDVs identified in Russia. At least 25 putative recombination events between a vaccine strain and a field strain were identified in the genome of GD01/2020, which could affect the virulence and transmissibility of the virus. These results suggested that a virulent vaccine-recombinant LSDV from an unknown origin was introduced into Xinjiang, China in 2019 and spread to Guangdong, China in 2020. This article is protected by copyright. All rights reserved.}, }
@article {pmid34927211, year = {2021}, author = {Islam, MM and Bhattacharya, R and Sarkar, B and Maiti, PK and Mahanty, S and Chaudhuri, P and Biswas, SR and Mandal, S}, title = {Different soil salinity imparts clear alteration in rhizospheric bacterial community dynamics in rice and peanut.}, journal = {Archives of microbiology}, volume = {204}, number = {1}, pages = {36}, pmid = {34927211}, issn = {1432-072X}, abstract = {The rhizospheric microbiome is capable of changing the physio-chemical properties of its own micro-environment and found to be indispensable in the overall health of the hostplant. The interplay between the rhizospheric environment and the microbiota residing therein tune the physiology of the associated plant. In this study, we have determined how the soil properties and the host-plant remains as an important parameter for microbial community dynamics in the rhizosphere of rice and peanut. In addition to check the physio-chemical parameters of the rhizospheric soil, we have also prepared the metagenomic DNA from each rhizospheric soil followed by high-throughput sequencing and sequence analysis to predict the OTUs that represents the community structure. The alpha-diversity of the bacterial community in the RRN sample was highest, while the lowest was in PRS sample. Actinobacteria is the most predominant phylum in PRN, PRS and RRN, whereas Acidobacteria in RRS. We found a clear shift in bacterial community over the rice and peanut rhizosphere and also over these host-rhizospheres from normal and high saline region. The rhizospheric bacterial community composition found to be affected by the close-by environmental factors. Thus, the rhizospheric bacterial community structure is related to both the adjoining soil characters and the type of the hosts.}, }
@article {pmid34927107, year = {2021}, author = {Cáceres, PFF and Vélez, LP and Junca, H and Moreno-Herrera, CX}, title = {Theobroma cacao L. agricultural soils with natural low and high cadmium (Cd) in Santander (Colombia), contain a persistent shared bacterial composition shaped by multiple soil variables and bacterial isolates highly resistant to Cd concentrations.}, journal = {Current research in microbial sciences}, volume = {2}, number = {}, pages = {100086}, doi = {10.1016/j.crmicr.2021.100086}, pmid = {34927107}, issn = {2666-5174}, abstract = {Heavy metals can be found in soil as natural components or as product of contaminations events; plants growing in soils are prone to bioaccumulate heavy metals on their biomass. Theobroma cacao L. can bioaccumulate cadmium (Cd) in the seed and could be in derived food products, it considered a human health risk; therefore, removal of Cd is desirable but not vet technically and economically feasible; only to avoid Cd in cocoa is by selecting lands plots exhibiting lower Cd concentrations in soils, imposing a serious limitation to farmers and regulators. The study of bacterial communities and isolation bacteria with tolerance and mechanisms to counteract the translocation of Cd to the parts of cocoa plant exhibits high relevance in Colombia economy and especially to companies producing chocolate and derivatives. Here, we explore bacterial communities associated with soils having relatively high natural Cd concentrations in a large agricultural cocoa plot located in the Santander region. We characterized the bacterial communities' compositions by amplicon 16S rRNA sequencing from metagenomics soil DNA and by culturing-based enumeration and isolation approaches. Culture-dependent techniques allowed the isolation of bacteria tolerant to Cd concentration, complement the information for Colombia, and expand the number of strains characterized with adaptive capacity against Cd with tolerance in a concentration of 120 mg/L, which represents the first capacity for Exiguobacterium sp., Ralstonia sp., Serratia sp., Dermacoccus sp., Klebsiella sp., Lactococcus sp. and Staphylococcus sp. In addition to confirming that there is a greater diversity of Cd-tolerant bacteria present in soils of farms cultivated with cocoa in Colombia. As for the results of new generation sequencing, they revealed that, the alpha-diversity in bacterial composition, according to the ANOVA, there are statistically significant differences of the bacterial communities present in the samples. Regarding Pearson correlation analysis, it was found the Shannon Simpson indices, have a positive correlation against OM, C, pH, Mn, C.E.C.I., Ca, P and negatively correlated with S; respect to bacterial community structure, a principal component analysis, which revealed that independent of the concentration of Cd present in soil samples, separates them according to pH value. Phyla to high abundance relative in all samples were Proteobacteria, Acidobacteriota, Actinobacteriota, Verrucomicrobiota, Myxococcota, Chloroflexi, Plactomycetota, Bacteroidota, Gemmatimonadota, Nitrospirota, Firmicutes and NB1_J; the bacteria genera with higher relative abundance (>0.5%) Nitrospira, candidatus Udaeobacter, Haliangium, Cupriavidus, MND1, Bacillus, Kitasatospora, Niveibacterium, Acidothermus, Burkholderia, Acidibacter, Terrimonas, Gaiella, candidatus Solibacter, Kitasatospora, Sphingomonas, Streptomyces, this genus with a relationship with the Cd tolerance process. After it, redundancy analysis was performed between the variation of the bacterial communities identified by dependent and independent techniques and edaphic soil variables, where their positive correlation was found against K, OM, C, Ca, pH (p<0.01) and P, C.E.C.I (p<0.05). For soil samples, the bacterial genera that make up the core community were identified, which are present in all samples as Nitrospira sp., Cupriavidus sp., Burkholderia sp., Haliangium sp., candidatus Udaeobacter, MND1, Kitasatospora, Acidothermus, Acidibacter, Streptomyces, Gaiella, candidatus Solibacter and Terramonas; the genera identified has a different and fundamental role in ecosystem functioning. The combination of different approaches offers new clues regarding the assessment of bacterial communities in soils cultivated with cocoa in soils with elevated Cd content in Colombia, and the ecological role and interplay of soil components and bacterial communities that contribute to modulate the effect of bioaccumulation in products.}, }
@article {pmid34926314, year = {2021}, author = {Liu, Y and Zhang, H and Tang, X and Jiang, X and Yan, X and Liu, X and Gong, J and Mew, K and Sun, H and Chen, X and Zou, Z and Chen, C and Qiu, J}, title = {Distinct Metagenomic Signatures in the SARS-CoV-2 Infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {706970}, doi = {10.3389/fcimb.2021.706970}, pmid = {34926314}, issn = {2235-2988}, abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can cause gastrointestinal symptoms in the patients, but the role of gut microbiota in SARS-CoV-2 infection remains unclear. Thus, in this study, we aim to investigate whether SARS-CoV-2 infection affects the composition and function of gut microbiota. In this study, we demonstrated for the first time that significant shifts in microbiome composition and function were appeared in both SARS-CoV-2-infected asymptomatic and symptomatic cases. The relative abundance of Candidatus_Saccharibacteria was significantly increased, whereas the levels of Fibrobacteres was remarkably reduced in SARS-CoV-2-infected cases. There was one bacterial species, Spirochaetes displayed the difference between patients and asymptomatic cases. On the genus level, Tyzzerella was the key species that remarkably increased in both symptomatic and asymptomatic cases. Analyses of genome annotations further revealed SARS-CoV-2 infection resulted in the significant 'functional dysbiosis' of gut microbiota, including metabolic pathway, regulatory pathway and biosynthesis of secondary metabolites etc. We also identified potential metagenomic markers to discriminate SARS-CoV-2-infected symptomatic and asymptomatic cases from healthy controls. These findings together suggest gut microbiota is of possible etiological and diagnostic importance for SARS-CoV-2 infection.}, }
@article {pmid34925807, year = {2021}, author = {Tsui, KC and Yen, TL and Huang, CJ and Hong, KJ}, title = {Lactobacillus rhamnosus GG as dietary supplement improved survival from lipopolysaccharides-induced sepsis in mice.}, journal = {Food science &amp; nutrition}, volume = {9}, number = {12}, pages = {6786-6793}, doi = {10.1002/fsn3.2630}, pmid = {34925807}, issn = {2048-7177}, abstract = {Sepsis is a state of host immune response triggered by virus or bacterial infection, in which the extent of regional and systemic inflammation and companion counter-inflammatory reactions determines disease outcomes. Probiotics are known for the immunomodulatory effect on allergic disorders, but it is not clear whether the beneficiary effect extends to sepsis and increases survival. In this mouse model, we injected intraperitoneally lipopolysaccharides (LPS) to induce sepsis, and investigated whether the pretreatment of Lactobacillus rhamnosus GG (LGG) contributed to host survival and examined the alteration of the gut microbiota and blood cytokines/chemokines profile before sepsis induction. Four-week-old male BALB/c mice were divided into two groups: one group were fed daily with LGG as a dietary supplement for fourteen days, whereas the other group with sterile water. Before sepsis induction, some mice from each group were killed to collect stool in the intestine and blood for microbial metagenomic and cytokine/chemokine analyses, respectively, and the rest were monitored afterward for mortality. The relative abundance of several families in the gut microbiota after LGG treatment was altered as well as the ratio of Firmicutes/Bacteroidetes. In addition, several pro-inflammatory cytokines such as G-CSF, IL7, IL15, and MCP1 were lower in the LGG group than in the control group. The survival rate following LPS-induced sepsis improved with LGG treatment. Our results indicated that dietary supplement of probiotic LGG improved survival from LPS-induced sepsis, most likely through pre-septic changes in the gut microbial constituents by LGG with reciprocal alteration of host immune system to a less reactive state to incoming pathogens.}, }
@article {pmid34925329, year = {2021}, author = {Guo, Y and Huang, X and Sun, X and Yu, Y and Wang, Y and Zhang, B and Cao, J and Wen, S and Li, Y and Wang, X and Cai, S and Xia, W and Wei, F and Duan, J and Dong, H and Guo, S and Zhang, F and Zheng, D and Sun, Z}, title = {The Underrated Salivary Virome of Men Who Have Sex With Men Infected With HIV.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {759253}, doi = {10.3389/fimmu.2021.759253}, pmid = {34925329}, issn = {1664-3224}, abstract = {Salivary virome is important for oral ecosystem, but there are few reports on people living with HIV. We performed metagenomic sequencing to compare composition and functional genes of salivary virobiota between one HIV-negative and four HIV-positive groups in which participants were all men who have sex with men (MSM) with different immunosuppression statuses (five samples per group) to find the evidence that salivary virobiota plays a role in the pathogenesis of oral disease. Acute-stage subjects achieved a positive result of HIV RNA, but HIV antibody negative or indeterminate, whereas individuals with mild, moderate, and severe immunosuppression exhibited CD4+ T-lymphocyte counts of at least 500, 200-499, and less than 200 cells/μL or opportunistic infection, respectively. The results showed the composition of salivary virus genera in subjects with mild immunosuppression was the most similar to that in healthy people, followed by that in the acute stage; under severe immunosuppression, virus genera were suppressed and more similar to that under moderate immunosuppression. Furthermore, abnormally high abundance of Lymphocryptovirus was particularly obvious in MSM with HIV infection. Analysis of KEGG Pathway revealed that Caulobacter cell cycle, which affects cell duplication, became shorter in HIV-positive subjects. It is worth noting that in acute-stage participants, protein digestion and absorption related to the anti-HIV-1 activity of secretory leukocyte protease inhibitor was increased. Moreover, in the severely immunosuppressed subjects, glutathione metabolism, which is associated with the activation of lymphocytes, was enhanced. Nevertheless, the ecological dysbiosis in HIV-positive salivary virobiota possibly depended on the changes in blood viral load, and salivary dysfunction of MSM infected with HIV may be related to CD4 counts. Ribonucleoside diphosphate reductase subunit M1 in purine metabolism was negatively correlated, though weakly, to CD4 counts, which may be related to the promotion of HIV-1 DNA synthesis in peripheral blood lymphocytes. 7-Cyano-7-deazaguanine synthase in folate biosynthesis was weakly positively correlated with HIV viral load, suggesting that this compound was produced excessively to correct oral dysfunction for maintaining normal cell development. Despite the limited number of samples, the present study provided insight into the potential role of salivary virome in the oral function of HIV infected MSM.}, }
@article {pmid34925263, year = {2021}, author = {Ghodhbane-Gtari, F and D'Angelo, T and Gueddou, A and Ghazouani, S and Gtari, M and Tisa, LS}, title = {Alone Yet Not Alone: Frankia Lives Under the Same Roof With Other Bacteria in Actinorhizal Nodules.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {749760}, doi = {10.3389/fmicb.2021.749760}, pmid = {34925263}, issn = {1664-302X}, abstract = {Actinorhizal plants host mutualistic symbionts of the nitrogen-fixing actinobacterial genus Frankia within nodule structures formed on their roots. Several plant-growth-promoting bacteria have also been isolated from actinorhizal root nodules, but little is known about them. We were interested investigating the in planta microbial community composition of actinorhizal root nodules using culture-independent techniques. To address this knowledge gap, 16S rRNA gene amplicon and shotgun metagenomic sequencing was performed on DNA from the nodules of Casuarina glauca. DNA was extracted from C. glauca nodules collected in three different sampling sites in Tunisia, along a gradient of aridity ranging from humid to arid. Sequencing libraries were prepared using Illumina NextEra technology and the Illumina HiSeq 2500 platform. Genome bins extracted from the metagenome were taxonomically and functionally profiled. Community structure based off preliminary 16S rRNA gene amplicon data was analyzed via the QIIME pipeline. Reconstructed genomes were comprised of members of Frankia, Micromonospora, Bacillus, Paenibacillus, Phyllobacterium, and Afipia. Frankia dominated the nodule community at the humid sampling site, while the absolute and relative prevalence of Frankia decreased at the semi-arid and arid sampling locations. Actinorhizal plants harbor similar non-Frankia plant-growth-promoting-bacteria as legumes and other plants. The data suggests that the prevalence of Frankia in the nodule community is influenced by environmental factors, with being less abundant under more arid environments.}, }
@article {pmid34923897, year = {2022}, author = {Bihl, S and de Goffau, M and Podlesny, D and Segata, N and Shanahan, F and Walter, J and Fricke, WF}, title = {When to suspect contamination rather than colonization - lessons from a putative fetal sheep microbiome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2005751}, doi = {10.1080/19490976.2021.2005751}, pmid = {34923897}, issn = {1949-0984}, abstract = {There is an ongoing controversy around the existence of a prenatal, fetal microbiome in humans, livestock, and other animals. The 'in utero microbial colonization' hypothesis challenges the clinical paradigm of the 'sterile womb' but has been criticized for its reliance on DNA-based evidence to detect microbiomes and the failure to conciliate the routine experimental derivation of germ-free animals from surgically resected embryos with a thriving fetal microbiome. In order to avoid the propagation of misinformation in the scientific literature, a critical assessment and careful review of newly published studies, particularly those that challenge the convincing current clinical dogma of the sterile womb, is of critical importance.We read with interest a recent publication that postulated the presence of a fetal microbiome in sheep, but questioned the plausibility of the reported findings and their meaningfulness to prove "microbial colonisation of the fetal gut […] in utero". We reanalyzed the published metagenomic and metatranscriptomic sequence data from the original publication and identified evidence for different types of contamination that affected all samples alike and could explain the reported findings without requiring the existence of a fetal microbiome.Our reanalysis challenges the reported findings as supportive of a prenatal fetal lamb microbiome. The shortcomings of the original analysis and data interpretation highlight common problems of low-biomass microbiome projects. We propose genomic independence of separate biological samples, i.e. distinctive profiles at the microbial strain level, as a potential new microbiome marker to increase confidence in metagenomics analyses of controversial low-biomass microbiomes.}, }
@article {pmid34923604, year = {2021}, author = {Sarkar, I and Kar, P and Sen, G and Chhetri, S and Bhattacharya, M and Bhattacharyya, S and Sen, A}, title = {Metagenomic outlooks of microbial dynamics influenced by organic manure in tea garden soils of North Bengal, India.}, journal = {Archives of microbiology}, volume = {204}, number = {1}, pages = {33}, pmid = {34923604}, issn = {1432-072X}, abstract = {Soil microbial diversity consisted of both culturable and non-culturable microbes. The cultivated microbes can be identified by conventional microbiological processes. However, that is not possible for the non-culturable ones. In those cases, next-generation sequencing (NGS)-based metagenomics become useful. In this study, we targeted two very popular tea gardens of Darjeeling hills-Makaibari (Mak) and Castleton (Cas). The main difference between these two study areas is the type of manure they use. Mak is solely an organic tea garden using all organic manure and fertilizers whereas Cas uses inorganic pesticides and fertilizers. The main aim was to compare the effect of organic manure over chemical fertilizers on the soil microbiomes. We have performed the 16 s metagenomics analysis based on the V3-V4 region. Downstream bioinformatics analysis including reverse ecology was performed. We found that the overall microbial diversity is higher in Mak compared to Cas. Moreover, the use of organic manure has reduced the population of pathogenic bacteria in Mak soil when compared to Cas soil. From the observations made through the metagenomics analysis of Mak and Cas soil samples, we may conclude that the application of organic manure supports the population of good bacteria in the soil which may eventually impact the tea garden workers' health.}, }
@article {pmid34923445, year = {2021}, author = {Pelivano, B and Bryson, S and Hunt, KA and Denecke, M and Stahl, DA and Winkler, M}, title = {Application of pyritic sludge with an anaerobic granule consortium for nitrate removal in low carbon systems.}, journal = {Water research}, volume = {209}, number = {}, pages = {117933}, doi = {10.1016/j.watres.2021.117933}, pmid = {34923445}, issn = {1879-2448}, abstract = {Granules recovered from a highly reduced anaerobic digester were capable of active nitrogen removal in the absence of exogenous electron donors, averaging 0.25 mg mgNO3--N /gVSS/d over 546 days of operation. Electron mass balance indicated that about half the influent nitrate was converted to ammonia via DNRA and another half denitrified. This capacity was associated with an onion-like structure of multiple layers enriched in reduced iron and sulfur, and a complex microbial community shown by metagenomic sequencing to consist of multiple physiological groups and associated activities, including methanogenesis, denitrification, dissimilatory nitrate reduction to ammonia (DNRA), iron oxidation and reduction, and sulfur reduction and oxidation. Nitrate reduction was supported by both entrained organic material and reduced iron and sulfur species, corresponding to 2.13 mg COD/gVSS/d. Batch incubations showed that approximately 15% of denitrified nitrate was coupled to the oxidation of sulfur derived from both sulfate respiration and granular material enriched in iron-sulfide. Inhibition of sulfate reduction resulted in redirection of electron flow to methanogenesis and, in combination with other batch tests, showed that these granules supported a complex microbial community in which cryptic redox cycles linked carbon, sulfur, and iron oxidation with nitrate, sulfate, iron, and carbon dioxide reduction. This system shows promise for treatment of nitrate contaminated ground water without addition of an external organic carbon source as well as wastewater treatment in combination with (granular) sludge elimination leading in a net reduction of solid treatment costs.}, }
@article {pmid34923019, year = {2021}, author = {Chen, X and Wang, J and Pan, C and Feng, L and Guo, Q and Chen, S and Xie, S}, title = {Metagenomic analysis reveals the response of microbial community in river sediment to accidental antimony contamination.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152484}, doi = {10.1016/j.scitotenv.2021.152484}, pmid = {34923019}, issn = {1879-1026}, abstract = {The mining of deposits containing metals like antimony (Sb) causes serious environmental issues that threaten human health and ecological systems. However, information on the effect of Sb on freshwater sediment microorganisms and the mechanism of microbial Sb resistance is still very limited. This was the first attempt to explore microbial communities in river sediments impacted by accidental Sb spill. Metagenomic analysis revealed the high relative abundance of Proteobacteria and Actinobacteria in all the studied river sediments, showing their advantage in resistance to Sb pollution. Under Sb stress, microbial functions related to DNA repair and ion transport were enhanced. Increase in heavy metal resistance genes (HMRGs), particularly Sb transport-related arsB gene, was observed at Sb spill-impacted sites. HMRGs were significantly correlated with ARGs and MGEs, and the abundant MGEs at Sb spill-impacted sites might contribute to the increase in HMRGs and ARGs via horizontal gene transfer. Deinococcus, Sphingopyxis and Paracoccus were identified as potential tolerant genera under Sb pressure and might be related to the transmission of HMRGs and ARGs. This study can add new insights towards the effect of accidental metal spill on sediment microbial community.}, }
@article {pmid34922301, year = {2021}, author = {Gabashvili, E and Kobakhidze, S and Chkhikvishvili, T and Tabatadze, L and Tsiklauri, R and Dadiani, K and Koulouris, S and Kotetishvili, M}, title = {Metagenomic and recombinationanalyses of antimicrobial resistance genes from recreational waters of Black Sea coastal areas and other marine environments unveil extensive evidence for their both intrageneric and intergeneric transmission across genetically very diverse microbial communities.}, journal = {Marine genomics}, volume = {61}, number = {}, pages = {100916}, doi = {10.1016/j.margen.2021.100916}, pmid = {34922301}, issn = {1876-7478}, abstract = {Microbial communities of marine coastal recreation waters have become large reservoirs of AMR genes (ARGs), contributing to the emergence and transmission of various zoonotic, foodborne and other infections that exhibit resistance to various antibiotics. Thus, it is highly imperative to determine ARGs assemblages as well as mechanisms and trajectories of their transmission across these microbial communities for our better understanding of the evolutionary trends of AMR (AMR). In this study, using metagenomics approaches, we screened for ARGs in recreation waters of the Black Sea coastal areas of the Batumi City (Georgia). Also, a large array of the recombination detection algorithms of the SplitsTree, RDP4, and GARD was applied to elucidate genetic recombination of ARGs and trajectories of their transmission across various marine microbial communities. The metagenomics analyses of sea water samples, obtained from across the above marine sites, could identify putative ARGs encoding for multidrug resistance efflux transporters mainly from the Major Facilitator and Resistance Nodulation Division superfamilies. The data, generated by SplitsTree (fit ≥95.619; bootstrap values ≥ 95; Phi p ≤ 0.0494), RDP4 (p ≤ 0.0490), and GARD, provided strong statistical evidence not only for intrageneric recombination of these ARGs, but also for their intergeneric recombination across fairly large and diverse microbial communities of marine environment. These bacteria included both human pathogenic and nonpathogenic species, exhibiting collectively the genera of Vibrio, Aeromonas, Synechococcus, Citromicrobium, Rhodobacteraceae, Pseudoalteromonas, Altererythrobacter, Erythrobacter, Altererythrobacter, Marivivens, Xuhuaishuia, and Loktanella. The above nonpathogenic bacteria are strongly suggested to contribute to ARGs transmission in marine ecosystems.}, }
@article {pmid34920748, year = {2021}, author = {Wu, S and Zhou, R and Ma, Y and Fang, Y and Xie, G and Gao, X and Xiao, Y and Liu, J and Fang, Z}, title = {Development of a consortium-based microbial agent beneficial to composting of distilled grain waste for Pleurotus ostreatus cultivation.}, journal = {Biotechnology for biofuels}, volume = {14}, number = {1}, pages = {242}, pmid = {34920748}, issn = {1754-6834}, support = {17030701059//Science and Technology Major Project of Anhui Province/ ; 2008085J12//the Science Fund for Distinguished Young Scholars of Anhui Province/ ; Y040418162//the Doctoral Research Start-up Funding of Anhui University/ ; }, abstract = {BACKGROUND: Pleurotus ostreatus is an edible mushroom popularly cultivated worldwide. Distilled grain waste (DGW) is a potential substrate for P. ostreatus cultivation. However, components in DGW restrict P. ostreatus mycelial growth. Therefore, a cost-effective approach to facilitate rapid P. ostreatus colonization on DGW substrate will benefit P. ostreatus cultivation and DGW recycling.<br><br>RESULTS: Five dominant indigenous bacteria, Sphingobacterium sp. X1, Ureibacillus sp. X2, Pseudoxanthomonas sp. X3, Geobacillus sp. X4, and Aeribacillus sp. X5, were isolated from DGW and selected to develop a consortium-based microbial agent to compost DGW for P. ostreatus cultivation. Microbial agent inoculation led to faster carbohydrate metabolism, a higher temperature (73.2 vs. 71.2 °C), a longer thermophilic phase (5 vs. 3 days), and significant dynamic changes in microbial community composition and diversity in composts than those of the controls. Metagenomic analysis showed the enhanced microbial metabolisms, such as xenobiotic biodegradation and metabolism and terpenoid and polyketide metabolism, during the mesophilic phase after microbial agent inoculation, which may facilitate the fungal colonization on the substrate. In accordance with the bioinformatic analysis, a faster colonization of P. ostreatus was observed in the composts with microbial inoculation than in control after composting for 48 h, as indicated from substantially higher fungal ergosterol content, faster lignocellulose degradation, and higher lignocellulase activities in the former than in the latter. The final mushroom yield shared no significant difference between composts with microbial inoculation and control, with 0.67 ± 0.05 and 0.60 ± 0.04 kg fresh mushroom/kg DGW, respectively (p > 0.05).<br><br>CONCLUSION: The consortium-based microbial agent comprised indigenous microorganisms showing application potential in composting DGW for providing substrate for P. ostreatus cultivation and will provide an alternative to facilitate DGW recycling.}, }
@article {pmid34920354, year = {2021}, author = {Szulc, J and Okrasa, M and Majchrzycka, K and Sulyok, M and Nowak, A and Szponar, B and Górczyńska, A and Ryngajłło, M and Gutarowska, B}, title = {Microbiological and toxicological hazard assessment in a waste sorting plant and proper respiratory protection.}, journal = {Journal of environmental management}, volume = {303}, number = {}, pages = {114257}, doi = {10.1016/j.jenvman.2021.114257}, pmid = {34920354}, issn = {1095-8630}, abstract = {Even though biological hazards in the work environments related to waste management were the subject of many scientific works, the knowledge of the topic is not extensive. This study aimed to conduct a comprehensive assessment of microbiological and toxicological hazards at the workstations in a waste sorting plant and develop guidelines for selecting filtering respiratory protective devices that would consider specific workplace conditions. The research included the assessment of quantity (culture method), diversity (high-throughput sequencing), and metabolites (endotoxin - gas chromatography-mass spectrometry; secondary metabolites - liquid chromatography tandem-mass spectrometry) of microorganisms occurring in the air and settled dust. Moreover, cytotoxicity of settled dust against a human epithelial lung cell line was determined with an MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. The research was performed in a waste sorting plant (Poland; 240,000 tons waste/year) at six workstations: two feeders, two pre-sorting cabins, secondary raw material press and organic fraction waste feeder for composting. The total dust concentration at tested workstations varied from 0.128 mg m-3 to 5.443 mg m-3. The number of microorganisms was between 9.23 × 104 CFU m-3 and 1.38 × 105 CFU m-3 for bacteria and between 1.43 × 105 CFU m-3 and 1.65 × 105 CFU m-3 for fungi, which suggests high microbial contamination of the sorting facility. The numbers of microorganisms in the air correlated very strongly (R2 from 0.70 to 0.94) with those observed in settled dust. Microorganisms representing Group 2 biological agents (acc. to Directive, 2000/54/EC), including Corynebacterium spp., Pseudomonas aeruginosa, Staphylococcus aureus, and others potentially hazardous to human health, were identified. The endotoxins concentration in settled dust ranged from 0.013 nmol LPS mg-1 to 0.048 nmol LPS mg-1. Seventeen (air) and 91 (settled dust) secondary metabolites characteristic, e.g., for moulds, bacteria, lichens, and plants were identified. All dust samples were cytotoxic (IC50 values of 8.66 and 56.15 mg ml-1 after 72 h). A flowchart of respiratory protective devices selection for biological hazards at the workstations in the waste sorting plant was proposed based on the completed tests to help determine the right type and use duration of the equipment.}, }
@article {pmid34920315, year = {2021}, author = {Fu, S and Yang, Q and Sheng, Y and Wang, Q and Wu, J and Qiu, Z and Lan, R and Wang, Y and Liu, Y}, title = {Metagenomics combined with comprehensive validation as a public health risk assessment tool for urban and agricultural run-off.}, journal = {Water research}, volume = {209}, number = {}, pages = {117941}, doi = {10.1016/j.watres.2021.117941}, pmid = {34920315}, issn = {1879-2448}, abstract = {Early detection of emerging and life-threatening pathogens circulating in complex environments is urgently required to combat infectious diseases. This study proposed a public health risk assessment workflow with three stages, pathogen screening, pathogen genotyping, and risk assessment. In stage one, pathogens were screened with metagenomic sequencing, microfluidic chip, and qPCR. In stage two, pathogens were isolated and genotyped with multi-locus sequence typing (MLST) or conventional PCR. Finally, virulence genes from metagenomic data were assessed for pathogenicity. Two regions (Donggang and Zhanjiang) with potential public health concerns were selected for evaluation, each of which comprised of one urban and one farming wastewater sampling location. Overall, metagenomic sequencing reflected the variation in the relative abundance of medically important bacteria. Over 90 bacterial pathogens were monitored in the metagenomic dataset, of which 56 species harbored virulence genes. In Donggang, a pathogenic Acinetobacter sp. reached high abundances in 2018 and 2020, whereas all pathogenic Vibrio spp. peaked in October 2019. In Zhanjiang, A. baumanni, and other Enterobacteriaceae species were abundantly present in 2019 and 2020, whereas Aeromonas and Vibrio spp. peaked in November-2017. Forty species were subsequently isolated and subtyped by MLST, half of which were prevalent genotypes in clinical data. Additionally, we identified the African Swine Fever Virus (ASFV) in water samples collected in 2017, ahead of the first reported ASFV outbreak in 2018 in China. RNA viruses like Hepatitis A virus (HAV) and Enterovirus 71 (EV71) were also detected, with concentrations peaking in April 2020 and April 2018, respectively. The dynamics of HAV and EV71 were consistent with local epidemic trends. Finally, based on the virulence gene profiles, our study identified the risk level in wastewater of two cities. This workflow illustrates the potential for an early warning of local epidemics, which helps to prioritize the preparedness for specific pathogens locally.}, }
@article {pmid34919575, year = {2021}, author = {Tamang, JP and Kharnaior, P and Pariyar, P and Thapa, N and Lar, N and Win, KS and Mar, A and Nyo, N}, title = {Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar.}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0260777}, doi = {10.1371/journal.pone.0260777}, pmid = {34919575}, issn = {1932-6203}, abstract = {Pe poke is a naturally fermented sticky soybean food of Myanmar. The present study was aimed to profile the whole microbial community structure and their predictive gene functionality of pe poke samples prepared in different fermentation periods viz. 3 day (3ds), 4 days (4ds), 5 days (5ds) and sun-dried sample (Sds). The pH of samples was 7.6 to 8.7, microbial load was 2.1-3.9 x 108 cfu/g with dynamic viscosity of 4.0±1.0 to 8.0±1.0cP. Metataxonomic profile of pe poke samples showed different domains viz. bacteria (99.08%), viruses (0.65%), eukaryota (0.08%), archaea (0.03%) and unclassified sequences (0.16%). Firmicutes (63.78%) was the most abundant phylum followed by Proteobacteria (29.54%) and Bacteroidetes (5.44%). Bacillus thermoamylovorans was significantly abundant in 3ds and 4ds (p<0.05); Ignatzschineria larvae was significantly abundant in 5ds (p<0.05), whereas, Bacillus subtilis was significantly abundant in Sds (p <0.05). A total of 172 species of Bacillus was detected. In minor abundance, the existence of bacteriophages, archaea, and eukaryotes were also detected. Alpha diversity analysis showed the highest Simpson's diversity index in Sds comparable to other samples. Similarly, a non-parametric Shannon's diversity index was also highest in Sds. Good's coverage of 0.99 was observed in all samples. Beta diversity analysis using PCoA showed no significant clustering. Several species were shared between samples and many species were unique to each sample. In KEGG database, a total number of 33 super-pathways and 173 metabolic sub-pathways were annotated from the metagenomic Open Reading Frames. Predictive functional features of pe poke metagenome revealed the genes for the synthesis and metabolism of wide range of bioactive compounds including various essential amino acids, different vitamins, and enzymes. Spearman's correlation was inferred between the abundant species and functional features.}, }
@article {pmid34919514, year = {2021}, author = {Amsalu, A and Sapula, SA and Whittall, JJ and Hart, BJ and Bell, JM and Turnidge, J and Venter, H}, title = {Worldwide distribution and environmental origin of the Adelaide imipenemase (AIM-1), a potent carbapenemase in Pseudomonas aeruginosa.}, journal = {Microbial genomics}, volume = {7}, number = {12}, pages = {}, doi = {10.1099/mgen.0.000715}, pmid = {34919514}, issn = {2057-5858}, abstract = {Carbapenems are potent broad-spectrum β-lactam antibiotics reserved for the treatment of serious infections caused by multidrug-resistant bacteria such as Pseudomonas aeruginosa. The surge in P. aeruginosa resistant to carbapenems is an urgent threat, as very few treatment options remain. Resistance to carbapenems is predominantly due to the presence of carbapenemase enzymes. The assessment of 147 P. aeruginosa isolates revealed that 32 isolates were carbapenem non-wild-type. These isolates were screened for carbapenem resistance genes using PCR. One isolate from wastewater contained the Adelaide imipenemase gene (bla AIM-1) and was compared phenotypically with a highly carbapenem-resistant clinical isolate containing the bla AIM-1 gene. A further investigation of wastewater samples from various local healthcare and non-healthcare sources as well as river water, using probe-based qPCR, revealed the presence of the bla AIM-1 gene in all the samples analysed. The widespread occurrence of bla AIM-1 throughout Adelaide hinted at the possibility of more generally extensive spread of this gene than originally thought. A blast search revealed the presence of the bla AIM-1 gene in Asia, North America and Europe. To elucidate the identity of the organism(s) carrying the bla AIM-1 gene, shotgun metagenomic sequencing was conducted on three wastewater samples from different locations. Comparison of these nucleotide sequences with a whole-genome sequence of a P. aeruginosa isolate revealed that, unlike the genetic environment and arrangement in P. aeruginosa, the bla AIM-1 gene was not carried as part of any mobile genetic elements. A phylogenetic tree constructed with the deduced amino acid sequences of AIM-1 suggested that the potential origin of the bla AIM-1 gene in P. aeruginosa might be the non-pathogenic environmental organism, Pseudoxanthomonas mexicana.}, }
@article {pmid34917059, year = {2021}, author = {Duffield, KR and Hunt, J and Sadd, BM and Sakaluk, SK and Oppert, B and Rosario, K and Behle, RW and Ramirez, JL}, title = {Active and Covert Infections of Cricket Iridovirus and Acheta domesticus Densovirus in Reared Gryllodes sigillatus Crickets.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {780796}, pmid = {34917059}, issn = {1664-302X}, abstract = {Interest in developing food, feed, and other useful products from farmed insects has gained remarkable momentum in the past decade. Crickets are an especially popular group of farmed insects due to their nutritional quality, ease of rearing, and utility. However, production of crickets as an emerging commodity has been severely impacted by entomopathogenic infections, about which we know little. Here, we identified and characterized an unknown entomopathogen causing mass mortality in a lab-reared population of Gryllodes sigillatus crickets, a species used as an alternative to the popular Acheta domesticus due to its claimed tolerance to prevalent entomopathogenic viruses. Microdissection of sick and healthy crickets coupled with metagenomics-based identification and real-time qPCR viral quantification indicated high levels of cricket iridovirus (CrIV) in a symptomatic population, and evidence of covert CrIV infections in a healthy population. Our study also identified covert infections of Acheta domesticus densovirus (AdDNV) in both populations of G. sigillatus. These results add to the foundational research needed to better understand the pathology of mass-reared insects and ultimately develop the prevention, mitigation, and intervention strategies needed for economical production of insects as a commodity.}, }
@article {pmid34917052, year = {2021}, author = {Bonny, P and Schaeffer, J and Besnard, A and Desdouits, M and Ngang, JJE and Le Guyader, FS}, title = {Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {770385}, pmid = {34917052}, issn = {1664-302X}, abstract = {Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8-15% of reads with most sequences (68-87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence.}, }
@article {pmid34917042, year = {2021}, author = {Bandara, AY and Weerasooriya, DK and Trexler, RV and Bell, TH and Esker, PD}, title = {Soybean Roots and Soil From High- and Low-Yielding Field Sites Have Different Microbiome Composition.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {675352}, pmid = {34917042}, issn = {1664-302X}, abstract = {The occurrence of high- (H) and low- (L) yielding field sites within a farm is a commonly observed phenomenon in soybean cultivation. Site topography, soil physical and chemical attributes, and soil/root-associated microbial composition can contribute to this phenomenon. In order to better understand the microbial dynamics associated with each site type (H/L), we collected bulk soil (BS), rhizosphere soil (RS), and soybean root (R) samples from historically high and low yield sites across eight Pennsylvania farms at V1 (first trifoliate) and R8 (maturity) soybean growth stages (SGS). We extracted DNA extracted from collected samples and performed high-throughput sequencing of PCR amplicons from both the fungal ITS and prokaryotic 16S rRNA gene regions. Sequences were then grouped into amplicon sequence variants (ASVs) and subjected to network analysis. Based on both ITS and 16S rRNA gene data, a greater network size and edges were observed for all sample types from H-sites compared to L-sites at both SGS. Network analysis suggested that the number of potential microbial interactions/associations were greater in samples from H-sites compared to L-sites. Diversity analyses indicated that site-type was not a main driver of alpha and beta diversity in soybean-associated microbial communities. L-sites contained a greater percentage of fungal phytopathogens (ex: Fusarium, Macrophomina, Septoria), while H-sites contained a greater percentage of mycoparasitic (ex: Trichoderma) and entomopathogenic (ex: Metarhizium) fungal genera. Furthermore, roots from H-sites possessed a greater percentage of Bradyrhizobium and genera known to contain plant growth promoting bacteria (ex: Flavobacterium, Duganella). Overall, our results revealed that there were differences in microbial composition in soil and roots from H- and L-sites across a variety of soybean farms. Based on our findings, we hypothesize that differences in microbial composition could have a causative relationship with observed within-farm variability in soybean yield.}, }
@article {pmid34915867, year = {2021}, author = {Anjos, WF and Lanes, GC and Azevedo, VA and Santos, AR}, title = {GENPPI: standalone software for creating protein interaction networks from genomes.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {596}, pmid = {34915867}, issn = {1471-2105}, mesh = {Animals ; Phylogeny ; *Protein Interaction Maps/genetics ; Sheep ; *Software ; }, abstract = {BACKGROUND: Bacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships capable of being annotated only from genomes are conserved gene neighbourhoods (CNs), phylogenetic profiles (PPs), and gene fusions. At present, there is no standalone software that enables networks of interactions among proteins to be created using these three evolutionary characteristics with efficient and effective results.<br><br>RESULTS: We developed GENPPI software for the ab initio prediction of interaction networks using predicted proteins from a genome. In our case study, we employed 50 genomes of the genus Corynebacterium. Based on the PP relationship, GENPPI differentiated genomes between the ovis and equi biovars of the species Corynebacterium pseudotuberculosis and created groups among the other species analysed. If we inspected only the CN relationship, we could not entirely separate biovars, only species. Our software GENPPI was determined to be efficient because, for example, it creates interaction networks from the central genomes of 50 species/lineages with an average size of 2200 genes in less than 40 min on a conventional computer. Moreover, the interaction networks that our software creates reflect correct evolutionary relationships between species, which we confirmed with average nucleotide identity analyses. Additionally, this software enables the user to define how he or she intends to explore the PP and CN characteristics through various parameters, enabling the creation of customized interaction networks. For instance, users can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the user's choice regarding which set of genomes they are going to study.<br><br>CONCLUSIONS: GENPPI can help fill the gap concerning the considerable number of novel genomes assembled monthly and our ability to process interaction networks considering the noncore genes for all completed genome versions. With GENPPI, a user dictates how many and how evolutionarily correlated the genomes answer a scientific query.}, }
@article {pmid34915851, year = {2021}, author = {Ren, D and Ren, C and Yao, R and Zhang, L and Liang, X and Li, G and Wang, J and Meng, X and Liu, J and Ye, Y and Li, H and Wen, S and Chen, Y and Zhou, D and He, X and Li, X and Lai, K and Li, Y and Gui, S}, title = {The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with sepsis.}, journal = {BMC infectious diseases}, volume = {21}, number = {1}, pages = {1257}, pmid = {34915851}, issn = {1471-2334}, support = {No.SZGSP006//Shenzhen Fund for Guangdong Provincical High-level Clinical Key Specialties/ ; No.SZSM20162011//Sanming Project of Medicine in Shenzhen/ ; No.20193357004//Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; JSGG20200207161928126//Shenzhen Science and Technology Innovation Commission for Research and Development Project/ ; }, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics ; Retrospective Studies ; *Sepsis/diagnosis ; }, abstract = {BACKGROUND: In this study, we aimed to perform a comprehensive analysis on the metagenomic next-generation sequencing for the etiological diagnosis of septic patients, and further to establish optimal read values for detecting common pathogens.<br><br>METHODS: In this single-center retrospective study, septic patients who underwent pathogen detection by both microbial culture and metagenomic next-generation sequencing in the intensive care unit of the Second People's Hospital of Shenzhen from June 24, 2015, to October 20, 2019, were included.<br><br>RESULTS: A total of 193 patients with 305 detected specimens were included in the final analysis. The results of metagenomic next-generation sequencing showed significantly higher positive rates in samples from disparate loci, including blood, bronchoalveolar lavage fluid, and cerebrospinal fluid, as well as in the determination of various pathogens. The optimal diagnostic reads were 2893, 1825.5, and 892.5 for Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, respectively.<br><br>CONCLUSIONS: The metagenomic next-generation sequencing is capable of identifying multiple pathogens in specimens from septic patients, and shows significantly higher positive rates than culture-based diagnostics. The optimal diagnostic reads for frequently detected microbes might be useful for the clinical application of metagenomic next-generation sequencing in terms of timely and accurately determining etiological pathogens for suspected and confirmed cases of sepsis due to well-performed data interpretation.}, }
@article {pmid34831411, year = {2021}, author = {Schierova, D and Roubalova, R and Kolar, M and Stehlikova, Z and Rob, F and Jackova, Z and Coufal, S and Thon, T and Mihula, M and Modrak, M and Kverka, M and Bajer, L and Kostovcikova, K and Drastich, P and Hercogova, J and Novakova, M and Vasatko, M and Lukas, M and Tlaskalova-Hogenova, H and Jiraskova Zakostelska, Z}, title = {Fecal Microbiome Changes and Specific Anti-Bacterial Response in Patients with IBD during Anti-TNF Therapy.}, journal = {Cells}, volume = {10}, number = {11}, pages = {}, pmid = {34831411}, issn = {2073-4409}, support = {grant number NV18-09-00493.//Ministry of Health of the Czech Republic/ ; }, mesh = {Adult ; Antibodies/blood ; Biodiversity ; Case-Control Studies ; Feces/*microbiology ; Female ; Fungi/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Inflammatory Bowel Diseases/blood/*drug therapy/*microbiology/surgery ; Interleukin-17/metabolism ; Leukocytes, Mononuclear/metabolism ; Male ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Tumor Necrosis Factor Inhibitors/*therapeutic use ; }, abstract = {Inflammatory bowel diseases (IBD) are chronic disorders of the gastrointestinal tract that have been linked to microbiome dysbiosis and immune system dysregulation. We investigated the longitudinal effect of anti-TNF therapy on gut microbiota composition and specific immune response to commensals in IBD patients. The study included 52 patients tracked over 38 weeks of therapy and 37 healthy controls (HC). To characterize the diversity and composition of the gut microbiota, we used amplicon sequencing of the V3V4 region of 16S rRNA for the bacterial community and of the ITS1 region for the fungal community. We measured total antibody levels as well as specific antibodies against assorted gut commensals by ELISA. We found diversity differences between HC, Crohn's disease, and ulcerative colitis patients. The bacterial community of patients with IBD was more similar to HC at the study endpoint, suggesting a beneficial shift in the microbiome in response to treatment. We identified factors such as disease severity, localization, and surgical intervention that significantly contribute to the observed changes in the gut bacteriome. Furthermore, we revealed increased IgM levels against specific gut commensals after anti-TNF treatment. In summary, this study, with its longitudinal design, brings insights into the course of anti-TNF therapy in patients with IBD and correlates the bacterial diversity with disease severity in patients with ulcerative colitis (UC).}, }
@article {pmid34782034, year = {2021}, author = {Thurman, CE and Klores, MM and Wolfe, AE and Poueymirou, WT and Levee, EM and Ericsson, AC and Franklin, CL and Reddyjarugu, B}, title = {Effect of Housing Condition and Diet on the Gut Microbiota of Weanling Immunocompromised Mice.}, journal = {Comparative medicine}, volume = {71}, number = {6}, pages = {485-491}, doi = {10.30802/AALAS-CM-21-000015}, pmid = {34782034}, issn = {1532-0820}, abstract = {Gastrointestinal microbiota are affected by a wide variety of extrinsic and intrinsic factors. In the husbandry of laboratory mice and design of experiments, controlling these factors where possible provides more reproducible results. However, the microbiome is dynamic, particularly in the weeks immediately after weaning. In this study, we characterized the baseline gastrointestinal microbiota of immunocompromised mice housed under standard conditions for our facility for 6 weeks after weaning, with housing either in an isolator or in individually ventilated cages and a common antibiotic diet (trimethoprim sulfamethoxazole). We compared these conditions to a group fed a standard diet and a group that was weaned to a standard diet then switched to antibiotic diet after 2 weeks. We found no clear effect of diet on richness and α diversity of the gastrointestinal microbiota. However, diet did affect which taxa were enriched at the end of the experiment. The change to antibiotic diet during the experiment did not convert the gastrointestinal microbiome to a state similar to mice consistently fed antibiotic diet, which may highlight the importance of the initial post-weaning period in the establishment of the gastrointestinal microbiome. We also observed a strong effect of housing type (isolator compared with individually ventilated cage) on the richness, α diversity, β diversity, and taxa enriched over the course of the experiment. Investigating whether the diet or microbiome affects a certain strain's phenotype is warranted in some cases. However, our findings do not suggest that maintaining immunocompromised mice on antibiotic feed has a clinical benefit when potential pathogens are operationally excluded, nor does it result in a more consistent or controlled microbiome in the post-weaning period.}, }
@article {pmid34562162, year = {2021}, author = {de Fátima Silva Lopes, H and Tu, Z and Sumi, H and Furukawa, H and Yumoto, I}, title = {Indigofera tinctoria leaf powder as a promising additive to improve indigo fermentation prepared with sukumo (composted Polygonum tinctorium leaves).}, journal = {World journal of microbiology &amp; biotechnology}, volume = {37}, number = {10}, pages = {179}, pmid = {34562162}, issn = {1573-0972}, support = {G-2020-3-035//Institute for Fermentation, Osaka/ ; }, mesh = {Bacteria, Anaerobic/genetics ; Coloring Agents/chemistry ; *Fermentation ; High-Throughput Nucleotide Sequencing ; Indigo Carmine/chemistry ; *Indigofera/chemistry/microbiology ; Metagenomics ; Microbiota/genetics ; Plant Extracts/chemistry ; Plant Leaves/chemistry/microbiology ; *Polygonum/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Being insoluble in the oxidize form, indigo dye must be solubilized by reduction for it to penetrate textile. One of the procedures is the reduction by natural bacterial fermentation. Sukumo, composted leaves of Polygonum tinctorium, is a natural source of indigo in Japan. Although sukumo has an intrinsic bacterial seed, the onset of indigo reduction with this material may vary greatly. Certain additives improve indigo fermentation. Here, we studied the effects of Indigofera tinctoria leaf powder (LP) on the initiation of indigo reduction, bacterial community, redox potential (ORP), and dyeing intensity in the initial stages and in aged fermentation fluids prepared with sukumo. I. tinctoria LP markedly decreased ORP at day 1 and stabilised it during early fermentation. These effects could be explained by the phytochemicals present in I. tinctoria LP that act as oxygen scavengers and electron mediators. Using next generation sequencing results, we observed differences in the bacterial community in sukumo fermentation treated with I. tinctoria LP, which was not influenced by the bacterial community in I. tinctoria LP per se. The concomitant decrease in Bacillaceae and increase in Proteinivoraceae at the onset of fermentation, increase in the ratio of facultative to obligate anaerobes (F/O ratio), or the total abundance of facultative anaerobes (F) or obligate anaerobes (O) (designated F + O) are vital for the initiation and maintenance of indigo reduction. Hence, I. tinctoria LP improved early indigo reduction by decreasing the ORP and hasten the appropriate transitions in the bacterial community in sukumo fermentation.}, }
@article {pmid34539647, year = {2021}, author = {Zhang, J and Tao, J and Gao, RN and Wei, ZY and He, YS and Ren, CY and Li, QC and Liu, YS and Wang, KW and Yang, G and Qian, C and Chen, JH}, title = {Cytotoxic T-Cell Trafficking Chemokine Profiles Correlate With Defined Mucosal Microbial Communities in Colorectal Cancer.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {715559}, pmid = {34539647}, issn = {1664-3224}, mesh = {Adult ; Aged ; Biomarkers ; CD8-Positive T-Lymphocytes/immunology/metabolism ; Chemokines/*metabolism ; Chemotaxis, Leukocyte/*immunology ; Colorectal Neoplasms/*etiology/*metabolism/pathology ; Computational Biology/methods ; Disease Progression ; Disease Susceptibility ; Female ; Fluorescent Antibody Technique ; Gastrointestinal Microbiome/*immunology ; Humans ; Immunohistochemistry ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Neoplasm Grading ; Neoplasm Staging ; T-Lymphocytes, Cytotoxic/*immunology/*metabolism ; }, abstract = {The involvement of gut microbiota in T-cell trafficking into tumor tissue of colorectal cancer (CRC) remains to be further elucidated. The current study aimed to evaluate the expression of major cytotoxic T-cell trafficking chemokines (CTTCs) and chemokine-associated microbiota profiles in both tumor and adjacent normal tissues during CRC progression. We analyzed the expression of chemokine C-X-C motif ligands 9, 10, and 11 (CXCL9, CXCL10, and CXCL11), and C-C motif ligand 5 (CCL5), characterized gut mucosa-associated microbiota (MAM), and investigated their correlations in CRC patients. Our results showed that the expression of CXCL9, CXCL10, and CXCL11 was significantly higher in tumor than in adjacent normal tissues in 136 CRC patients. Notably, the high expression of CXCL9 in tumor tissues was associated with enhanced CD8+ T-cell infiltration and improved survival. Moreover, the MAM in tumor tissues showed reduction of microbial diversity and increase of oral bacteria. Microbial network analysis identified differences in microbial composition and structure between tumor and adjacent normal tissues. In addition, stronger associations between oral bacteria and other gut microbes were observed. Furthermore, the correlation analysis between the defined MAM and individual CTTCs showed that the CTTCs' correlated operational taxonomic units (OTUs) in tumor and adjacent normal tissues rarely overlap with each other. Notably, all the enriched OTUs were positively correlated with the CTTCs in either tumor or adjacent normal tissues. Our findings demonstrated stronger interactions between oral bacteria and gut microbes, and a shifted correlation pattern between MAM and major CTTCs in tumor tissues, underlining possible mechanisms of gut microbiota-host interaction in CRC.}, }
@article {pmid34484230, year = {2021}, author = {Que, Y and Cao, M and He, J and Zhang, Q and Chen, Q and Yan, C and Lin, A and Yang, L and Wu, Z and Zhu, D and Chen, F and Chen, Z and Xiao, C and Hou, K and Zhang, B}, title = {Gut Bacterial Characteristics of Patients With Type 2 Diabetes Mellitus and the Application Potential.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {722206}, pmid = {34484230}, issn = {1664-3224}, mesh = {Case-Control Studies ; Diabetes Mellitus, Type 2/*complications/metabolism ; Dysbiosis/*etiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Probiotics ; RNA, Ribosomal, 16S ; ROC Curve ; }, abstract = {Type 2 diabetes mellitus (T2DM) is a complex disorder comprehensively influenced by genetic and environmental risk, and research increasingly has indicated the role of microbial dysbiosis in T2DM pathogenesis. However, studies comparing the microbiome characteristics between T2DM and healthy controls have reported inconsistent results. To further identify and describe the characteristics of the intestinal flora of T2DM patients, we performed a systematic review and meta-analysis of stool microbial profiles to discern and describe microbial dysbiosis in T2DM and to explore heterogeneity among 7 studies (600 T2DM cases, 543 controls, 1143 samples in total). Using a random effects model and a fixed effects model, we observed significant differences in beta diversity, but not alpha diversity, between individuals with T2DM and controls. We identified various operational taxonomic unit (OTUs) and bacterial genera with significant odds ratios for T2DM. The T2DM signatures derived from a single study by stepwise feature selection could be applied in other studies. By training on multiple studies, we improved the detection accuracy and disease specificity for T2DM. We also discuss the relationship between T2DM-enriched or T2DM-depleted genera and probiotics and provide new ideas for diabetes prevention and improvement.}, }
@article {pmid34406857, year = {2021}, author = {Taylor, LJ and Dothard, MI and Rubel, MA and Allen, AA and Hwang, Y and Roche, AM and Graham-Wooten, J and Fitzgerald, AS and Khatib, LA and Ranciaro, A and Thompson, SR and Beggs, WR and Campbell, MC and Mokone, GG and Mpoloka, SW and Fokunang, C and Njamnshi, AK and Mbunwe, E and Woldemeskel, D and Belay, G and Nyambo, T and Tishkoff, SA and Collman, RG and Bushman, FD}, title = {Redondovirus Diversity and Evolution on Global, Individual, and Molecular Scales.}, journal = {Journal of virology}, volume = {95}, number = {21}, pages = {e0081721}, pmid = {34406857}, issn = {1098-5514}, support = {T32 AI007532/AI/NIAID NIH HHS/United States ; 9299//Wenner-Gren Foundation (WGF)/ ; R33HL137063-S1//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; P30 AI045008/AI/NIAID NIH HHS/United States ; BCS-1540432//National Science Foundation (NSF)/ ; R33HL137063//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 1-19-VSN-02//American Diabetes Association/ ; 5T32AI007532-18//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R35 GM134957/GM/NIGMS NIH HHS/United States ; R33 HL137063/HL/NHLBI NIH HHS/United States ; T32AI007324//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R25 GM071745/GM/NIGMS NIH HHS/United States ; T32 AI007324/AI/NIAID NIH HHS/United States ; R25GM071745//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM134957-01//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Africa/epidemiology ; Biodiversity ; Critical Illness ; DNA Virus Infections/epidemiology/*virology ; DNA Viruses/*classification/*genetics/*metabolism ; DNA-Binding Proteins/metabolism ; Evolution, Molecular ; Genome, Viral ; Humans ; Metagenomics ; Mouth/*virology ; Periodontitis/virology ; Phylogeny ; Prevalence ; Respiratory System/*virology ; Rural Population ; Saliva/*virology ; United States/epidemiology ; Viral Proteins/metabolism ; }, abstract = {Redondoviridae is a newly established family of circular Rep-encoding single-stranded (CRESS) DNA viruses found in the human ororespiratory tract. Redondoviruses were previously found in ∼15% of respiratory specimens from U.S. urban subjects; levels were elevated in individuals with periodontitis or critical illness. Here, we report higher redondovirus prevalence in saliva samples: four rural African populations showed 61 to 82% prevalence, and an urban U.S. population showed 32% prevalence. Longitudinal, limiting-dilution single-genome sequencing revealed diverse strains of both redondovirus species (Brisavirus and Vientovirus) in single individuals, persistence over time, and evidence of intergenomic recombination. Computational analysis of viral genomes identified a recombination hot spot associated with a conserved potential DNA stem-loop structure. To assess the possible role of this site in recombination, we carried out in vitro studies which showed that this potential stem-loop was cleaved by the virus-encoded Rep protein. In addition, in reconstructed reactions, a Rep-DNA covalent intermediate was shown to mediate DNA strand transfer at this site. Thus, redondoviruses are highly prevalent in humans, found in individuals on multiple continents, heterogeneous even within individuals and encode a Rep protein implicated in facilitating recombination. IMPORTANCE Redondoviridae is a recently established family of DNA viruses predominantly found in the human respiratory tract and associated with multiple clinical conditions. In this study, we found high redondovirus prevalence in saliva from urban North American individuals and nonindustrialized African populations in Botswana, Cameroon, Ethiopia, and Tanzania. Individuals on both continents harbored both known redondovirus species. Global prevalence of both species suggests that redondoviruses have long been associated with humans but have remained undetected until recently due to their divergent genomes. By sequencing single redondovirus genomes in longitudinally sampled humans, we found that redondoviruses persisted over time within subjects and likely evolve by recombination. The Rep protein encoded by redondoviruses catalyzes multiple reactions in vitro, consistent with a role in mediating DNA replication and recombination. In summary, we identify high redondovirus prevalence in humans across multiple continents, longitudinal heterogeneity and persistence, and potential mechanisms of redondovirus evolution by recombination.}, }
@article {pmid34367180, year = {2021}, author = {Lv, L and Jiang, H and Chen, X and Wang, Q and Wang, K and Ye, J and Li, Y and Fang, D and Lu, Y and Yang, L and Gu, S and Chen, J and Diao, H and Yan, R and Li, L}, title = {The Salivary Microbiota of Patients With Primary Biliary Cholangitis Is Distinctive and Pathogenic.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {713647}, pmid = {34367180}, issn = {1664-3224}, mesh = {Biomarkers ; Case-Control Studies ; Chemokines/metabolism ; Cytokines/metabolism ; Dysbiosis/*etiology ; Female ; *Host Microbial Interactions/immunology ; Humans ; Inflammation Mediators/metabolism ; Keratinocytes/metabolism ; Liver Cirrhosis, Biliary/*complications/diagnosis/etiology/metabolism ; Liver Function Tests ; Male ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Saliva/*microbiology ; }, abstract = {The role of host-microbiota interactions in primary biliary cholangitis (PBC) has received increased attention. However, the impact of PBC on the oral microbiota and contribution of the oral microbiota to PBC are unclear. In this study, thirty-nine PBC patients without other diseases and 37 healthy controls (HCs) were enrolled and tested for liver functions and haematological variables. Saliva specimens were collected before and after brushing, microbiota was determined using 16S rDNA sequencing, metabolomics was profiled using Gas Chromatography-Mass Spectrometer (GC-MS), 80 cytokines were assayed using biochips, and inflammation inducibility was evaluated using OKF6 keratinocytes and THP-1 macrophages. Finally, the effect of ultrasonic scaling on PBC was estimated. Compared with HCs, PBC saliva had enriched taxa such as Bacteroidetes, Campylobacter, Prevotella and Veillonella and depleted taxa such as Enterococcaceae, Granulicatella, Rothia and Streptococcus. PBC saliva also had enriched sCD163, enriched metabolites such as 2-aminomalonic acid and 1-dodecanol, and depleted metabolites such as dodecanoic acid and propylene glycol. sCD163, 4-hydroxybenzeneacetic acid and 2-aminomalonic acid were significantly correlated with salivary cytokines, bacteria and metabolites. Salivary Veillonellaceae members, 2-aminomalonic acid, and sCD163 were positively correlated with liver function indicators such as serum alkaline phosphatase (ALP), aspartate aminotransferase (AST) and alanine aminotransferase (ALT). PBC salivary microbes induced more soluble interleukin (IL)-6 receptor α (sIL-6Rα), sIL-6Rβ and tumour necrosis factor ligand superfamily (TNFSF)13B from OKF6 keratinocytes, and PBC salivary supernatant induced more IL-6, IL-10, granulocyte-macrophage colony-stimulating factor (GM-CSF), chemokine (C-C motif) ligand (CCL)13, C-X-C motif chemokine (CXC)L1 and CXCL16 from THP-1 macrophages. Toothbrushing significantly reduced the expression of inflammatory cytokines such as IL-1β, IL-8 and TNF-α and harmful metabolites such as cadaverine and putrescine in PBC but not HC saliva after P-value correction. The levels of ALP and bilirubin in PBC serum were decreased after ultrasonic scaling. Together, PBC patients show significant alterations in their salivary microbiota, likely representing one cause and treatment target of oral inflammation and worsening liver functions.}, }
@article {pmid34915282, year = {2021}, author = {Kang, Y and Chen, S and Chen, Y and Tian, L and Wu, Q and Zheng, M and Li, Z}, title = {Alterations of fecal antibiotic resistome in COVID-19 patients after empirical antibiotic exposure.}, journal = {International journal of hygiene and environmental health}, volume = {240}, number = {}, pages = {113882}, doi = {10.1016/j.ijheh.2021.113882}, pmid = {34915282}, issn = {1618-131X}, abstract = {As the COVID-19 pandemic spread globally, the consumption of antibiotics increased. However, no studies exist evaluating the effect of antibiotics use on the antibiotic resistance of intestinal flora in COVID-19 patients during the pandemic. To explore this issue, we collected 15 metagenomic data of fecal samples from healthy controls (HCs) with no use history of antibiotics, 23 metagenomic data of fecal samples from COVID-19 patients who received empirical antibiotics [COVID-19 (abx+)], 18 metagenomic data of fecal samples from antibiotics-naïve COVID-19 patients [COVID-19 (abx-)], and six metagenomic data of fecal samples from patients with community-acquired pneumonia [PC (abx+)] from the Sequence Read Archive database. A total of 513 antibiotic-resistant gene (ARG) subtypes of 18 ARG types were found. Antibiotic treatment resulted in a significant increase in the abundance of ARGs in intestinal flora of COVID-19 patients and markedly altered the composition of ARG profiles. Grouped comparisons of pairs of Bray-Curtis dissimilarity values demonstrated that the dissimilarity of the HC versus the COVID-19 (abx+) group was significantly higher than the dissimilarity of the HC versus the COVID-19 (abx-) group. The mexF, mexD, OXA_209, major facilitator superfamily transporter, and EmrB_QacA family major facilitator transporter genes were the discriminative ARG subtypes for the COVID-19 (abx+) group. IS621, qacEdelta, transposase, and ISCR were significantly increased in COVID-19 (abx+) group; they greatly contributed toward explaining variation in the relative abundance of ARG types. Overall, our data provide important insights into the effect of antibiotics use on the antibiotic resistance of COVID-19 patients during the COVID-19 epidemic.}, }
@article {pmid34915114, year = {2021}, author = {Maleki, M and Ariaeenejad, S and Hosseini Salekdeh, G}, title = {Efficient saccharification of ionic liquid-pretreated rice straw in a one-pot system using novel metagenomics derived cellulases.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {126536}, doi = {10.1016/j.biortech.2021.126536}, pmid = {34915114}, issn = {1873-2976}, abstract = {Ionic liquids (ILs)-resistant cellulase enzymes can facilitate the saccharification of IL- pretreated biomass in a one-pot wash-free method. Using a bioinformatics approach, two cellulases, Persicel7 and Persicel8, with convincing evidence for ionic liquid tolerance were identified. Subsequently, these enzymes were heterologously expressed and biochemically characterized. Persicel7 and Persicel8 exhibited endo-β-1, 4-glucanase activity and were resistant to inhibitors and several organic solvents. Their activity in 10% (v/v) 1-ethyl-3-methylimidazolium chloride and 1-butyl-3-methylimidazolium chloride were 130% higher compared with IL-free control. The half-life of cellulases was improved up to 11-fold when incubated with 20% (v/v) solution of ion liquids. In addition, a one-pot IL-pretreatment and enzymatic saccharification of rice straw enhanced the saccharification rate by 33% compared to the untreated reaction. The Persicel7 and Persicel8 unique properties make them attractive candidates for industrial applications, particularly hydrolyzing ion liquid activated biomass in a one-pot system.}, }
@article {pmid34915097, year = {2021}, author = {Delacuvellerie, A and Géron, A and Gobert, S and Wattiez, R}, title = {New insights into the functioning and structure of the PE and PP plastispheres from the Mediterranean Sea.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {118678}, doi = {10.1016/j.envpol.2021.118678}, pmid = {34915097}, issn = {1873-6424}, abstract = {Plastic debris are accumulating in the marine environment and aggregate microorganisms that form a new ecosystem called the plastisphere. Better understanding the plastisphere is crucial as it has self-sufficient organization and, carries pathogens or organisms that may be involved in the pollutant adsorption and/or plastic degradation. To date, the plastisphere is mainly described at the taxonomic level and the functioning of its microbial communities still remains poorly documented. In this work, metagenomic and metaproteomic analyzes were performed on the plastisphere of polypropylene and polyethylene plastic debris sampled on a pebble beach from the Mediterranean Sea. Our results confirmed that the plastisphere was organized as self-sufficient ecosystems containing highly active primary producers and heterotrophs and predators such as nematode. Interestingly, the chemical composition of the polymer did not impact the structure of the microbial communities but rather influenced the functions expressed. Despite the fact that the presence of hydrocarbon degrader bacteria was observed in the metagenome, polymer degradation metabolisms were not detected at the protein level. Finally, hydrocarbon degrader (i.e., Alcanivorax) and pathogenic bacteria (i.e., Vibrionaceae) were observed in the plastispheres but were not very active as no proteins involved in polymer degradation or pathogeny were detected. This work brings a new insight into the functioning of the microbial plastisphere developed on plastic marine debris.}, }
@article {pmid34915016, year = {2021}, author = {Kang, M and Yang, J and Kim, S and Park, J and Kim, M and Park, W}, title = {Occurrence of antibiotic resistance genes and multidrug-resistant bacteria during wastewater treatment processes.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152331}, doi = {10.1016/j.scitotenv.2021.152331}, pmid = {34915016}, issn = {1879-1026}, abstract = {Wastewater treatment plants (WWTPs) constantly receive a wide variety of contaminants, including pharmaceuticals, and are potential reservoirs of antibiotic resistance genes (ARGs). This favors the development of multidrug-resistant bacteria (MRB) through horizontal gene transfer. Samples from five different WWTP processes were collected in September 2020 and January 2021 to monitor ARG resistomes and culturable MRB in the presence of eight different antibiotics. Nanopore-based ARG abundance and bacterial community analyses suggested that ARG accumulation favors the generation of MRB. Activated and mixed sludges tended to have lower bacterial diversity and ARG abundance because of selective forces that favored the growth of specific microorganisms during aeration processes. Escherichia strains enriched in WWTPs (up to 71%) were dominant in all the samples, whereas Cloacamonas species were highly abundant only in anaerobically digested sludge samples (60%-79%). Two ARG types [sulfonamide resistance genes (sul1) and aminoglycoside resistance genes (aadA1, aadA13, and aadA2)] were prevalent in all the processes. The total counts of culturable MRB, such as Niabella, Enterococcus, Bacillus, and Chryseobacterium species, gradually increased during aerobic WWTP processes. Genomic analyses of all MRB isolated from the samples revealed that the resistome of Enterococcus species harbored the highest number of ARGs (7-18 ARGs), commonly encoding ant(6)-la, lnu(B), erm(B), and tet(S/M). On the other hand, Niablella strains possibly had intrinsic resistant phenotypes without ARGs. All MRB possessed ARGs originating from the same mobile genetic elements, suggesting that WWTPs are hotspots for the migration of ARGs and emergence of MRB.}, }
@article {pmid34914355, year = {2021}, author = {Sun, J and Barrett, H and Hall, DR and Kutarna, S and Wu, X and Wang, Y and Peng, H}, title = {Ecological Role of 6OH-BDE47: Is It a Chemical Offense Molecule Mediated by Enoyl-ACP Reductases?.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.1c05718}, pmid = {34914355}, issn = {1520-5851}, abstract = {Although hydroxylated polybrominated diphenyl ethers (OH-BDEs) are among the most abundant natural organobromine compounds, the fundamental biological rationale for marine organisms to produce OH-BDEs remains elusive. Herein, we demonstrated that natural OH-BDEs exerted strong antibacterial activities against Escherichia coli by inhibiting enoyl-[acyl-carrier-protein] reductase (FabI), while anthropogenic OH-BDEs were inactive. Distinct from E. coli, OH-BDE-producing marine γ-proteobacteria including Marinomonas mediterranea MMB-1 (MMB-1) and Pseudoalteromonas luteoviolacea 2ta16 (Pl2ta16) exhibited resistance to 6OH-BDE47. An alternative enoyl-[acyl-carrier-protein] (ACP) reductase, FabV, was detected in all three OH-BDE-producing marine γ-proteobacteria. Thermal stability and protein affinity purification studies revealed that 6OH-BDE47 did not bind to recombinant or endogenous FabV of MMB-1 or Pl2ta16, demonstrating that FabV was the primary mechanism for OH-BDE-producing marine γ-proteobacteria to be resistant to 6OH-BDE47. To further confirm if the laboratory results were evidenced in the field, the 16S rRNA sequencing and metagenomics data from seven field-collected marine sponges were analyzed. Notably, the two Clade 4 sponges containing high concentrations of 6OH-BDE47 exhibited a distinct microbiome community structure compared to the other analyzed clades. Correspondingly, FabV was found to be selectively enriched in the same Clade 4 sponges. The merged evidence from the laboratory experiments and field studies demonstrated that 6OH-BDE47 may act as a chemical offense molecule in marine sponges.}, }
@article {pmid34914113, year = {2021}, author = {Salami, M and Sadeghian Motahar, SF and Ariaeenejad, S and Sheykh Abdollahzadeh Mamaghani, A and Kavousi, K and Moosavi-Movahedi, AA and Hosseini Salekdeh, G}, title = {The novel homologue of the human α-glucosidase inhibited by the non-germinated and germinated quinoa protein hydrolysates after in vitro gastrointestinal digestion.}, journal = {Journal of food biochemistry}, volume = {}, number = {}, pages = {e14030}, doi = {10.1111/jfbc.14030}, pmid = {34914113}, issn = {1745-4514}, support = {//Agricultural Biotechnology Research Institute of Iran/ ; }, abstract = {Quinoa (Chenopodium quinoa Willd) is a potential source of protein with ideal amino acid profiles which its bioactive compounds can be improved during germination and gastrointestinal digestion. The present investigation studies the impact of germination for 24 hr and simulated gastrointestinal digestion on α-glucosidase inhibitory activity of the quinoa protein and bioactive peptides against the novel homologue of human α-glucosidase, PersiAlpha-GL1. The sprouted quinoa after gastroduodenal digestion was the most effective α-glucosidase inhibitor showing 81.10% α-glucosidase inhibition at concentration 4 mg/ml with the half inhibition rate (IC50) of 0.07 mg/ml. Based on the kinetic analysis, both the germinated and non-germinated samples before and after digestion were competitive-type inhibitors of α-glucosidase. Results of this study showed the improved α-glucosidase inhibitory activity of the quinoa bioactive peptides after germination and gastrointestinal digestion and highlighted the potential of metagenome-derived PersiAlpha-GL1 as a novel homologue of the human α-glucosidase for developing the future anti-diabetic drugs. PRACTICAL APPLICATIONS: This study aimed to evaluate the effect of germination and gastrointestinal digestion of the quinoa protein and bioactive peptides on α-glucosidase inhibitory activity against the novel PersiAlpha-GL1. Metagenomic data were used to identify the novel α-glucosidase structurally and functionally homologue of human intestinal. The results showed the highest inhibition on PersiAlpha-GL1 by a germinated quinoa after gastroduodenal digestion and confirmed the potential of PersiAlpha-GL1 to enhance the effectiveness of the anti-diabetic drugs for industrial application.}, }
@article {pmid34912870, year = {2021}, author = {Hayashi, T and Yamashita, T and Takahashi, T and Tabata, T and Watanabe, H and Gotoh, Y and Shinohara, M and Kami, K and Tanaka, H and Matsumoto, K and Hayashi, T and Yamada, T and Hirata, KI}, title = {Uncovering the Role of Gut Microbiota in Amino Acid Metabolic Disturbances in Heart Failure Through Metagenomic Analysis.}, journal = {Frontiers in cardiovascular medicine}, volume = {8}, number = {}, pages = {789325}, doi = {10.3389/fcvm.2021.789325}, pmid = {34912870}, issn = {2297-055X}, abstract = {Aims: Circulating amino acid (AA) abnormalities serve as predictors of adverse outcomes in patients with heart failure (HF). However, the role of the gut microbiota in AA disturbances remains unknown. Thus, we investigated gut microbial functions and their associations with AA metabolic alterations in patients with HF. Methods and Results: We performed whole-genome shotgun sequencing of fecal samples and mass spectrometry-based profiling of AAs in patients with compensated HF. Plasma levels of total essential AAs (EAAs) and histidine were significantly lower in patients with HF than in control subjects. HF patients also displayed increased and decreased abundance of gut microbial genes involved in the degradation and biosynthesis, respectively, of EAAs, including branched-chain AAs (BCAAs) and histidine. Importantly, a significant positive correlation was observed between the abundance of microbial genes involved in BCAA biosynthesis and plasma BCAA levels in patients with HF, but not in controls. Moreover, network analysis revealed that the depletion of Eubacterium and Prevotella, which harbor genes for BCAA and histidine biosynthesis, contributed to decreased abundance of microbial genes involved in the biosynthesis of those EAAs in patients with HF. Conclusions: The present study demonstrated the relationship between gut microbiota and AA metabolic disturbances in patients with HF.}, }
@article {pmid34912314, year = {2021}, author = {Guo, Y and Li, L and Li, Z and Sun, L and Wang, H}, title = {Tropheryma whipplei Detection by Nanopore Sequencing in Patients With Interstitial Lung Disease.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {760696}, doi = {10.3389/fmicb.2021.760696}, pmid = {34912314}, issn = {1664-302X}, abstract = {Tropheryma whipplei is a bacterium associated with Whipple's disease, which commonly manifests as weight loss, arthralgia, and diarrhea. The most frequently involved organs comprise the heart and eyes, in addition to the central nervous system. Few studies have explored the relationship between T. whipplei and pneumonia. Herein, we report three patients with interstitial lung disease (ILD) of unknown cause, whose bronchoalveolar lavage fluid (BALF) were evaluated via Nanopore sequencing. In our in-house BALF Nanopore platform, human DNA was removed with saponin, to improve the reads ratio of microorganisms/host. T. whipplei was the sole or most abundant pathogen in all the patients, comprising 1,385, 826, and 285 reads. The positive result was confirmed via quantitative polymerase chain reaction (PCR) with two pairs of primers (cycle threshold value: 33.26/36.29; 31.68/32.01; 28.82/28.80) and Sanger sequencing. To our knowledge, this is the first report of T. whipplei detection using Nanopore-based sequencing. The turnaround time was approximately 6-8 h in clinical laboratories, including less than 1 h for analysis. In conclusion, the results of this study confirm that Nanopore sequencing can rapidly detect rare pathogens, to improve clinical diagnosis. In addition, diagnosis of Whipple's disease should be combined other laboratory findings, such as periodic acid-Schiff (PAS) staining, and considered a possibility in middle-aged men presenting with ILD and a clinical history of unexplained arthralgia and/or fever.}, }
@article {pmid34912116, year = {2021}, author = {Coelho, LP and Alves, R and Del Río, ÁR and Myers, PN and Cantalapiedra, CP and Giner-Lamia, J and Schmidt, TS and Mende, DR and Orakov, A and Letunic, I and Hildebrand, F and Van Rossum, T and Forslund, SK and Khedkar, S and Maistrenko, OM and Pan, S and Jia, L and Ferretti, P and Sunagawa, S and Zhao, XM and Nielsen, HB and Huerta-Cepas, J and Bork, P}, title = {Towards the biogeography of prokaryotic genes.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {34912116}, issn = {1476-4687}, abstract = {Microbial genes encode the majority of the functional repertoire of life on earth. However, despite increasing efforts in metagenomic sequencing of various habitats1-3, little is known about the distribution of genes across the global biosphere, with implications for human and planetary health. Here we constructed a non-redundant gene catalogue of 303 million species-level genes (clustered at 95% nucleotide identity) from 13,174 publicly available metagenomes across 14 major habitats and use it to show that most genes are specific to a single habitat. The small fraction of genes found in multiple habitats is enriched in antibiotic-resistance genes and markers for mobile genetic elements. By further clustering these species-level genes into 32 million protein families, we observed that a small fraction of these families contain the majority of the genes (0.6% of families account for 50% of the genes). The majority of species-level genes and protein families are rare. Furthermore, species-level genes, and in particular the rare ones, show low rates of positive (adaptive) selection, supporting a model in which most genetic variability observed within each protein family is neutral or nearly neutral.}, }
@article {pmid34911987, year = {2021}, author = {Soto-Giron, MJ and Kim, JN and Schott, E and Tahmin, C and Ishoey, T and Mincer, TJ and DeWalt, J and Toledo, G}, title = {The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {24017}, pmid = {34911987}, issn = {2045-2322}, abstract = {Plant microbiomes have been extensively studied for their agricultural relevance on growth promotion and pathogenesis, but little is known about their role as part of the diet when fresh fruits and vegetables are consumed raw. Most studies describing these communities are based on 16S rRNA gene amplicon surveys, limiting our understanding of the taxonomic resolution at the species level and functional capabilities. In this study, we characterized microbes colonizing tomatoes, spinach, brined olives, and dried figs using shotgun metagenomics. We recovered metagenome-assembled genomes of novel lactic acid bacteria from green olives and identified high intra- and inter-specific diversity of Pseudomonas in tomatoes. All samples were colonized by Pseudomonas, consistent with other reports with distinct community structure. Functional characterization showed the presence of enzymes involved in vitamin and short chain fatty acid metabolism and degradation of diverse carbohydrate substrates including plant fibers. The dominant bacterial members were isolated, sequenced, and mapped to its metagenome confirming their identity and indicating the microbiota is culturable. Our results reveal high genetic diversity, previously uncultured genera, and specific functions reflecting a likely plant host association. This study highlights the potential that plant microbes can play when consumed as part of our diet and proposes these as transient contributors to the gut microbiome.}, }
@article {pmid34911967, year = {2021}, author = {Hoque, MN and Sarkar, MMH and Rahman, MS and Akter, S and Banu, TA and Goswami, B and Jahan, I and Hossain, MS and Shamsuzzaman, AKM and Nafisa, T and Molla, MMA and Yeasmin, M and Ghosh, AK and Osman, E and Alam, SKS and Uzzaman, MS and Habib, MA and Mahmud, ASM and Crandall, KA and Islam, T and Khan, MS}, title = {SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {24042}, pmid = {34911967}, issn = {2045-2322}, abstract = {The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic functions. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 patients = 8, recovered humans = 7, and healthy people = 7) were collected, and underwent to RNAseq-based metagenomic investigation. Our RNAseq data mapped to 2281 bacterial species (including 1477, 919 and 676 in healthy, COVID-19 and recovered metagenomes, respectively) indicating a distinct microbiome dysbiosis. The COVID-19 and recovered samples included 67% and 77% opportunistic bacterial species, respectively compared to healthy controls. Notably, 79% commensal bacterial species found in healthy controls were not detected in COVID-19 and recovered people. Similar dysbiosis was also found in viral and archaeal fraction of the nasopharyngeal microbiomes. We also detected several altered metabolic pathways and functional genes in the progression and pathophysiology of COVID-19. The nasopharyngeal microbiome dysbiosis and their genomic features determined by our RNAseq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease.}, }
@article {pmid34911849, year = {2021}, author = {Feng, S and Luo, P and Huang, S and Ou, Z}, title = {Diagnosis and treatment for a case of Legionella longbeachae severe pneumonia and literature review.}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {46}, number = {10}, pages = {1167-1171}, doi = {10.11817/j.issn.1672-7347.2021.200629}, pmid = {34911849}, issn = {1672-7347}, abstract = {As a type of Legionella bacteria, Legionella longbeachae bacteria can lead to very rare legionella disease case in China with clinical characteristics, such as no typical early clinical symptoms, strong toxicity, high mortality, and not easy to detect by conventional etiology. A case of severe pneumonia caused by Legionella longbeachae infection was confirmed by bronchoalveolar lavage fluid pathogen metagenomics, and the patient's condition was improved after targeted anti-infection treatment. At present, our understanding in Legionella longbeachae severe pneumonia is limited. The diagnosis and treatment process of the patient with severe pneumonia of Legionella longbeachaeis retrospectively analyzed and the relevant literature was reviewed to provide the experience for its future diagnosis and treatment.}, }
@article {pmid34911583, year = {2021}, author = {Allali, I and Abotsi, RE and Tow, LA and Thabane, L and Zar, HJ and Mulder, NM and Nicol, MP}, title = {Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {241}, pmid = {34911583}, issn = {2049-2618}, abstract = {BACKGROUND: The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies.<br><br>METHODOLOGY: We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction.<br><br>RESULTS: We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168).<br><br>CONCLUSIONS: There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.}, }
@article {pmid34910917, year = {2021}, author = {Wurster, JI and Peterson, RL and Brown, CE and Penumutchu, S and Guzior, DV and Neugebauer, K and Sano, WH and Sebastian, MM and Quinn, RA and Belenky, P}, title = {Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis.}, journal = {Cell reports}, volume = {37}, number = {11}, pages = {110113}, doi = {10.1016/j.celrep.2021.110113}, pmid = {34910917}, issn = {2211-1247}, abstract = {It is well established in the microbiome field that antibiotic (ATB) use and metabolic disease both impact the structure and function of the gut microbiome. But how host and microbial metabolism interacts with ATB susceptibility to affect the resulting dysbiosis remains poorly understood. In a streptozotocin-induced model of hyperglycemia (HG), we use a combined metagenomic, metatranscriptomic, and metabolomic approach to profile changes in microbiome taxonomic composition, transcriptional activity, and metabolite abundance both pre- and post-ATB challenge. We find that HG impacts both microbiome structure and metabolism, ultimately increasing susceptibility to amoxicillin. HG exacerbates drug-induced dysbiosis and increases both phosphotransferase system activity and energy catabolism compared to controls. Finally, HG and ATB co-treatment increases pathogen susceptibility and reduces survival in a Salmonella enterica infection model. Our data demonstrate that induced HG is sufficient to modify the cecal metabolite pool, worsen the severity of ATB dysbiosis, and decrease colonization resistance.}, }
@article {pmid34910161, year = {2021}, author = {Williams, CJ and Torquati, L and Li, Z and Lea, RA and Croci, I and Keating, E and Little, JP and Eynon, N and Coombes, JS}, title = {Oligofructose-enriched inulin intake, gut microbiome characteristics and the V̇O2peak response to high-intensity interval training in healthy inactive adults.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1093/jn/nxab426}, pmid = {34910161}, issn = {1541-6100}, abstract = {BACKGROUND: The gut microbiome has been associated with cardiorespiratory fitness.<br><br>OBJECTIVE: To assess the effects of oligofructose (FOS)-enriched inulin supplementation on the gut microbiome and the peak oxygen uptake (V̇O2peak) response to high-intensity interval training (HIIT).<br><br>METHODS: The study was a randomized controlled trial. Forty sedentary and apparently healthy adults (n = 31 females; age = 31.8±9.8 years, BMI = 25.9±4.3 kg·m-2) were randomly allocated to: i) six weeks of supervised HIIT (4×4 min bouts at 85-95% HRpeak, interspersed with 3 min of active recovery, 3·week-1) + 12 g·day-1 of FOS-enriched inulin (HIIT-I) or ii) six weeks of supervised HIIT (3·week-1, 4×4 min bouts) + 12 g·day-1 of maltodextrin/placebo (HIIT-P). Each participant completed an incremental treadmill test to assess V̇O2peak and ventilatory thresholds (VTs), provided a stool and blood sample, and completed a 24-hour diet recall and food frequency questionnaire before and after the intervention. Gut microbiome analyses were performed using metagenomic sequencing. Fecal short-chain fatty acids were measured by mass spectrometry.<br><br>RESULTS: There were no differences in the mean change in V̇O2peak response between groups (P = 0.58). HIIT-I had a greater improvement in VTs than HIIT-P (VT1 - lactate accumulation: mean difference +4.3% and VT2 - lactate threshold: +4.2%, P<0.05). HIIT-I had a greater increase in the abundance of Bifidobacterium taxa (False Discovery Rate (FDR) <0.05) and several metabolic processes related to exercise capacity (FDR <0.05). Exploratory analysis of merged data found participants with a greater response to HIIT (V̇O2peak ≥3.5mL·kg-¹·min-¹) had a 2.2-fold greater mean abundance of gellan degradation pathways (FDR <0.05) and a greater, but not significant, abundance of B. Uniformis spp. (P<0.00023, FDR = 0.08).<br><br>CONCLUSIONS: FOS-enriched inulin supplementation did not potentiate HIIT-induced improvements in V̇O2peak, but led to gut microbiome changes possibly associated with greater ventilatory threshold improvements in healthy inactive adults. Gellan degradation pathways and B.uniformis spp. were associated with greater V̇O2peak responses to HIIT.<br><br>CLINICAL TRIALS REGISTER: ACTRN12618000501246.}, }
@article {pmid34909748, year = {2021}, author = {Rangu, S and Lee, JJ and Hu, W and Bittinger, K and Castelo-Soccio, L}, title = {Understanding the Gut Microbiota in Pediatric Patients with Alopecia Areata and their Siblings: A Pilot Study.}, journal = {JID innovations}, volume = {1}, number = {4}, pages = {100051}, doi = {10.1016/j.xjidi.2021.100051}, pmid = {34909748}, issn = {2667-0267}, abstract = {A cross-sectional study of 41 children aged 4-17 years with alopecia areata and 41 of their siblings without alopecia areata was conducted. A total of 51% had the Severity of Alopecia Tool scores in the range of 0-25%, 12% had scores between 26% and 49%, and 36% had scores between 75% and 100%. The fecal microbiome was characterized using shotgun metagenomic sequencing. A comparison of alpha and beta diversity yielded a small but statistically significant difference on the basis of Jaccard distance, which measures species presence and absence between samples. However, a follow-up analysis did not reveal the particular species that were present more often in one group. The relative abundance of one species, Ruminococcus bicirculans, was decreased in patients with alopecia areata relative to that in their sibling controls. An analysis of gene ortholog abundance identified 20 orthologs that were different between groups, including spore germination genes and genes for metal transportation. The associations reported in this study support a view of pediatric alopecia areata as a systemic disease that has effects on hair but also leads to internal changes, including differences in the gut microbiome.}, }
@article {pmid34908857, year = {2021}, author = {Wu, S and Hu, W and Xiao, W and Li, Y and Huang, Y and Zhang, X}, title = {Metagenomic Next-Generation Sequencing Assists in the Diagnosis of Gardnerella vaginalis in Males with Pleural Effusion and Lung Infection: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {14}, number = {}, pages = {5253-5259}, doi = {10.2147/IDR.S337248}, pmid = {34908857}, issn = {1178-6973}, abstract = {Gardnerella vaginalis is a pathogen responsible for bacterial vaginosis, which is commonly found in female vaginas and rarely causes infections outside the female genitalia. Here, we report the use of metagenomic next-generation sequencing (mNGS) to detect and confirm pulmonary infection and pleural effusion caused by G. vaginalis in a 47-year-old man. The patient's symptoms and imaging improved after 2 weeks of oral ornidazole, and he was cured after 3 months. Overall, the findings of this case demonstrate that mNGS is a useful tool for diagnosis of unexplained lung infections and pleural effusions. Its effectiveness in rapid and accurate etiological diagnosis and monitoring of diseases can allow detection of the etiology of difficult cases that return negative results after traditional cultures.}, }
@article {pmid34908504, year = {2021}, author = {Kang, Y and Ji, X and Guo, L and Xia, H and Yang, X and Xie, Z and Shi, X and Wu, R and Feng, D and Wang, C and Chen, M and Zhang, W and Wei, H and Guan, Y and Ye, K and Zhao, G}, title = {Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0076921}, doi = {10.1128/Spectrum.00769-21}, pmid = {34908504}, issn = {2165-0497}, abstract = {Cerebrospinal fluid (CSF) circulating in the human central nervous system has long been considered aseptic in healthy individuals, because normally, the blood-brain barrier can protect against microbial invasions. However, this dogma has been called into question by several reports that microbes were identified in human brains, raising the question of whether there is a microbial community in the CSF of healthy individuals without neurological diseases. Here, we collected CSF samples and other samples, including one-to-one matched oral and skin swab samples (positive controls), from 23 pregnant women aged between 23 and 40 years. Normal saline samples (negative controls), sterile swabs, and extraction buffer samples (contamination controls) were also collected. Twelve of the CSF specimens were also used to evaluate the physiological activities of detected microbes. Metagenomic and metatranscriptomic sequencing was performed in these 116 specimens. A total of 620 nonredundant microbes were detected, which were dominated by bacteria (74.6%) and viruses (24.2%), while in CSF samples, metagenomic sequencing found only 26 nonredundant microbes, including one eukaryote, four bacteria, and 21 viruses (mostly bacteriophages). The beta diversity of microbes compared between CSF metagenomic samples and other types of samples (except negative controls) was significantly different from that of the CSF self-comparison. In addition, there was no active or viable microbe in the matched metagenomic and metatranscriptomic sequencing of CSF specimens after subtracting those also found in normal saline, DNA extraction buffer, and skin swab specimens. In conclusion, our results showed no strong evidence of a colonized microbial community present in the CSF of healthy individuals. IMPORTANCE The microbiome is prevalent throughout human bodies, with profound health implications. However, it remains unclear whether it is present and active in human CSF, which has been long considered aseptic due to the blood-brain barrier. Here, we applied unbiased metagenomic and metatranscriptomic sequencing to detect the presence of a microbiome in CSF collected from 23 pregnant women with matched controls. Analysis of 116 specimens found no strong evidence to support the presence of a colonized microbiome in CSF. Our findings will strengthen our understanding of the internal environment of the CSF in healthy people, which has strong implications for human health, especially for neurological infections and disorders, and will help further disease diagnostics, prevention, and therapeutics in clinical settings.}, }
@article {pmid34908468, year = {2021}, author = {Ballard, MB and Mercado-Evans, V and Marunde, MG and Nwanosike, H and Zulk, J and Patras, KA}, title = {Group B Streptococcus CAMP Factor Does Not Contribute to Interactions with the Vaginal Epithelium and Is Dispensable for Vaginal Colonization in Mice.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0105821}, doi = {10.1128/Spectrum.01058-21}, pmid = {34908468}, issn = {2165-0497}, abstract = {The Gram-positive pathogen group B Streptococcus (GBS) is a leading cause of neonatal bacterial infections, preterm birth, and stillbirth. Although maternal GBS vaginal colonization is a risk factor for GBS-associated adverse birth outcomes, mechanisms promoting GBS vaginal persistence are not fully defined. GBS possesses a broadly conserved small molecule, CAMP factor, that is co-hemolytic in the presence of Staphylococcus aureus sphingomyelinase C. While this co-hemolytic reaction is commonly used by clinical laboratories to identify GBS, the contribution of CAMP factor to GBS vaginal persistence is unknown. Using in vitro biofilm, adherence and invasion assays with immortalized human vaginal epithelial VK2 cells, and a mouse model of GBS vaginal colonization, we tested the contribution of CAMP factor using GBS strain COH1 and its isogenic CAMP-deficient mutant (Δcfb). We found no evidence for CAMP factor involvement in GBS biofilm formation, or adherence, invasion, or cytotoxicity toward VK2 cells in the presence or absence of S. aureus. Additionally, there was no difference in vaginal burdens or persistence between COH1 and Δcfb strains in a murine colonization model. In summary, our results using in vitro human cell lines and murine models do not support a critical role for CAMP factor in promoting GBS vaginal colonization. IMPORTANCE Group B Streptococcus (GBS) remains a pervasive pathogen for pregnant women and their newborns. Maternal screening and intrapartum antibiotic prophylaxis to GBS-positive mothers have reduced, but not eliminated GBS neonatal disease, and have not impacted GBS-associated preterm birth or stillbirth. Additionally, this antibiotic exposure is associated with adverse effects on the maternal and neonatal microbiota. Identifying key GBS factors important for maternal vaginal colonization will foster development of more targeted, alternative therapies to antibiotic treatment. Here, we investigate the contribution of a broadly conserved GBS determinant, CAMP factor, to GBS vaginal colonization and find that CAMP factor is unlikely to be a biological target to control maternal GBS colonization.}, }
@article {pmid34908121, year = {2021}, author = {Miao, Y and Liu, F and Hou, T and Liu, Y}, title = {Virtifier: A deep learning-based identifier for viral sequences from metagenomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btab845}, pmid = {34908121}, issn = {1367-4811}, abstract = {MOTIVATION: Viruses, the most abundant biological entities on earth, are important components of microbial communities, and as major human pathogens, they are responsible for human mortality and morbidity. The identification of viral sequences from metagenomes is critical for viral analysis. As massive quantities of short sequences are generated by next-generation sequencing (NGS), most methods utilize discrete and sparse one-hot vectors to encode nucleotide sequences, which are usually ineffective in viral identification.<br><br>RESULTS: In this paper, Virtifier, a deep learning-based viral identifier for sequences from metagenomic data, is proposed. It includes a meaningful nucleotide sequence encoding method named Seq2Vec and a variant viral sequence predictor with an attention-based Long Short-Term Memory (LSTM) network. By utilizing a fully trained embedding matrix to encode codons, Seq2Vec can efficiently extract the relationships among those codons in a nucleotide sequence. Combined with an attention layer, the LSTM neural network can further analyze the codon relationships and sift the parts that contribute to the final features. Experimental results of three datasets have shown that Virtifier can accurately identify short viral sequences (< 500 bp) from metagenomes, surpassing three widely used methods, VirFinder, DeepVirFinder and PPR-Meta. Meanwhile, a comparable performance was achieved by Virtifier at longer lengths (> 5,000bp).<br><br>AVAILABILITY: A Python implementation of Virtifier and the Python code developed for this study have been provided on Github https://github.com/crazyinter/Seq2Vec.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid34907334, year = {2021}, author = {Tamashiro, R and Strange, L and Schnackenberg, K and Santos, J and Gadalla, H and Zhao, L and Li, EC and Hill, E and Hill, B and Sidhu, G and Kirst, M and Walker, C and Wang, GP}, title = {Stability of healthy subgingival microbiome across space and time.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23987}, pmid = {34907334}, issn = {2045-2322}, abstract = {The subgingival microbiome is one of the most stable microbial ecosystems in the human body. Alterations in the subgingival microbiome have been associated with periodontal disease, but their variations over time and between different subgingival sites in periodontally healthy individuals have not been well described. We performed extensive, longitudinal sampling of the subgingival microbiome from five periodontally healthy individuals to define baseline spatial and temporal variations. A total of 251 subgingival samples from 5 subjects were collected over 6-12 months and deep sequenced. The overall microbial diversity and composition differed significantly between individuals. Within each individual, we observed considerable differences in microbiome composition between different subgingival sites. However, for a given site, the microbiome was remarkably stable over time, and this stability was associated with increased microbial diversity but was inversely correlated with the enrichment of putative periodontal pathogens. In contrast to microbiome composition, the predicted functional metagenome was similar across space and time, suggesting that periodontal health is associated with shared gene functions encoded by different microbiome consortia that are individualized. To our knowledge, this is one of the most detailed longitudinal analysis of the healthy subgingival microbiome to date that examined the longitudinal variability of different subgingival sites within individuals. These results suggest that a single measurement of the healthy subgingival microbiome at a given site can provide long term information of the microbial composition and functional potential, but sampling of each site is necessary to define the composition and community structure at individual subgingival sites.}, }
@article {pmid34906258, year = {2021}, author = {Ingala, MR and Simmons, NB and Dunbar, M and Wultsch, C and Krampis, K and Perkins, SL}, title = {You are more than what you eat: potentially adaptive enrichment of microbiome functions across bat dietary niches.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {82}, pmid = {34906258}, issn = {2524-4671}, support = {Grant-in-aid of Research//American Society of Mammalogists/ ; TEC 2018 Exploration Fund Grant//Explorers Club/ ; 2017 Grant-in-aid of Research//Society for Integrative and Comparative Biology/ ; Grant-in-aid of Research//Sigma Xi/ ; RGGS Research Assistantship//American Museum of Natural History/ ; CSU-AAUP Travel Grant//AAUP Foundation/ ; }, abstract = {BACKGROUND: Animals evolved in a microbial world, and their gut microbial symbionts have played a role in their ecological diversification. While many recent studies report patterns of phylosymbiosis between hosts and their gut bacteria, fewer studies examine the potentially adaptive functional contributions of these microbes to the dietary habits of their hosts. In this study, we examined predicted metabolic pathways in the gut bacteria of more than 500 individual bats belonging to 60 species and compare the enrichment of these functions across hosts with distinct dietary ecologies.<br><br>RESULTS: We found that predicted microbiome functions were differentially enriched across hosts with different diets. Using a machine-learning approach, we also found that inferred microbiome functions could be used to predict specialized host diets with reasonable accuracy. We detected a relationship between both host phylogeny and diet with respect to microbiome functional repertoires. Because many predicted functions could potentially fill nutritional gaps for bats with specialized diets, we considered pathways discriminating dietary niches as traits of the host and fit them to comparative phylogenetic models of evolution. Our results suggest that some, but not all, predicted microbiome functions may evolve toward adaptive optima and thus be visible to the forces of natural selection operating on hosts over evolutionary time.<br><br>CONCLUSIONS: Our results suggest that bats with specialized diets may partially rely on their gut microbes to fulfill or augment critical nutritional pathways, including essential amino acid synthesis, fatty acid biosynthesis, and the generation of cofactors and vitamins essential for proper nutrition. Our work adds to a growing body of literature suggesting that animal microbiomes are structured by a combination of ecological and evolutionary processes and sets the stage for future metagenomic and metabolic characterization of the bat microbiome to explore links between bacterial metabolism and host nutrition.}, }
@article {pmid34906246, year = {2021}, author = {Chaudhari, NM and Overholt, WA and Figueroa-Gonzalez, PA and Taubert, M and Bornemann, TLV and Probst, AJ and Hölzer, M and Marz, M and Küsel, K}, title = {The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers.}, journal = {Environmental microbiome}, volume = {16}, number = {1}, pages = {24}, pmid = {34906246}, issn = {2524-6372}, support = {SFB 1076 -Project Number 218627073//deutsche forschungsgemeinschaft/ ; FZT 118 - 202548816//deutsche forschungsgemeinschaft/ ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//deutsche forschungsgemeinschaft/ ; Nachwuchsgruppe Dr. Alexander Probst//ministerium für kultur und wissenschaft des landes nordrhein-westfalen/ ; }, abstract = {BACKGROUND: The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges.<br><br>RESULTS: Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1 µm filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1 µm fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2 µm fractions. On average, Patescibacteria enriched in the smaller 0.1 µm filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2 µm fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota).<br><br>CONCLUSION: Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to attach multiple hosts just long enough to loot or exchange supplies.}, }
@article {pmid34906228, year = {2021}, author = {Shin, J and Noh, JR and Choe, D and Lee, N and Song, Y and Cho, S and Kang, EJ and Go, MJ and Ha, SK and Chang, DH and Kim, JH and Kim, YH and Kim, KS and Jung, H and Kim, MH and Sung, BH and Lee, SG and Lee, DH and Kim, BC and Lee, CH and Cho, BK}, title = {Ageing and rejuvenation models reveal changes in key microbial communities associated with healthy ageing.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {240}, pmid = {34906228}, issn = {2049-2618}, support = {2018M3A9H3024759//ministry of science and ict, south korea/ ; 2019M3A9F3065867//ministry of science and ict, south korea/ ; 2015M3C9A4053394//ministry of science and ict, south korea/ ; KGM5402113//Korea Research Institute of Bioscience and Biotechnology/ ; }, abstract = {BACKGROUND: The gut microbiota is associated with diverse age-related disorders. Several rejuvenation methods, such as probiotic administration and faecal microbiota transplantation, have been applied to alter the gut microbiome and promote healthy ageing. Nevertheless, prolongation of the health span of aged mice by remodelling the gut microbiome remains challenging.<br><br>RESULTS: Here, we report the changes in gut microbial communities and their functions in mouse models during ageing and three rejuvenation procedures including co-housing, serum-injection and parabiosis. Our results showed that the compositional structure and gene abundance of the intestinal microbiota changed dynamically during the ageing process. Through the three rejuvenation procedures, we observed that the microbial community and intestinal immunity of aged mice were comparable to those of young mice. The results of metagenomic data analysis underscore the importance of the high abundance of Akkermansia and the butyrate biosynthesis pathway in the rejuvenated mouse group. Furthermore, oral administration of Akkermansia sufficiently ameliorated the senescence-related phenotype in the intestinal systems in aged mice and extended the health span, as evidenced by the frailty index and restoration of muscle atrophy.<br><br>CONCLUSIONS: In conclusion, the changes in key microbial communities and their functions during ageing and three rejuvenation procedures, and the increase in the healthy lifespan of aged mice by oral administration of Akkermansia. Our results provide a rationale for developing therapeutic strategies to achieve healthy active ageing. Video abstract.}, }
@article {pmid34905647, year = {2021}, author = {Wang, G and Gao, Q and Yang, Y and Hobbie, SE and Reich, PB and Zhou, J}, title = {Soil enzymes as indicators of soil function: a step toward greater realism in microbial ecological modeling.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16036}, pmid = {34905647}, issn = {1365-2486}, abstract = {Soil carbon (C) and nitrogen (N) cycles and their complex responses to environmental changes have received increasing attention. However, large uncertainties in model predictions remain, partially due to the lack of explicit representation and parameterization of microbial processes. One great challenge is to effectively integrate rich microbial functional traits into ecosystem modeling for better predictions. Here, using soil enzymes as indicators of soil function, we developed a competitive dynamic enzyme allocation scheme and detailed enzyme-mediated soil inorganic N processes in the Microbial-ENzyme Decomposition (MEND) model. We conducted a rigorous calibration and validation of MEND with diverse soil C-N fluxes, microbial C:N ratios, and functional gene abundances from a 12-year CO2 ×N grassland experiment (BioCON) in Minnesota, USA. In addition to accurately simulating soil CO2 fluxes and multiple N variables, the model correctly predicted microbial C:N ratios and their negative response to enriched N supply. Model validation further showed that, compared to the changes in simulated enzyme concentrations and decomposition rates, the changes in simulated activities of eight C-N associated enzymes were better explained by the measured gene abundances in responses to elevated atmospheric CO2 concentration. Our results demonstrated that using enzymes as indicators of soil function and validating model predictions with functional gene abundance in ecosystem modeling can provide a basis for testing hypotheses about microbially-mediated biogeochemical processes in response to environmental changes. Further development and applications of the modeling framework presented here will enable microbial ecologists to address ecosystem-level questions beyond empirical observations, toward more predictive understanding, an ultimate goal of microbial ecology.}, }
@article {pmid34905206, year = {2022}, author = {Raza, A and Wu, Q}, title = {Diagnosis of Viral Diseases Using Deep Sequencing and Metagenomics Analyses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2400}, number = {}, pages = {225-243}, pmid = {34905206}, issn = {1940-6029}, abstract = {Viruses are ubiquitous in nature and exist in a variety of habitats. The advancement in sequencing technologies has revolutionized the understanding of viral biodiversity associated with plant diseases. Deep sequencing combined with metagenomics is a powerful approach that has proven to be revolutionary in the last decade and involves the direct analysis of viral genomes present in a diseased tissue sample. This protocol describes the details of RNA extraction and purification from wild rice plant and their yield, RNA purity, and integrity assessment. As a final step, bioinformatics data analysis including demultiplexing, quality control, de novo transcriptome assembly, taxonomic allocation and read mapping following Illumina HiSeq small and total RNA sequencing are described. Furthermore, the total RNAs extraction protocol and an additional ribosomal rRNAs depletion step which are significantly important for viral genomes construction are provided.}, }
@article {pmid34905112, year = {2021}, author = {Jiang, C and Tanaka, M and Nishikawa, S and Mino, S and Romalde, JL and Thompson, FL and Gomez-Gil, B and Sawabe, T}, title = {Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach.}, journal = {Current microbiology}, volume = {79}, number = {1}, pages = {10}, pmid = {34905112}, issn = {1432-0991}, support = {19H03041//KAKEN/ ; }, abstract = {Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, "Vibrio Clade 3.0," the second update of the molecular phylogenetic analysis was performed based on nucleotide sequences of eight housekeeping genes (8-HKGs) retrieved from genome sequences, including 22 newly determined genomes. A total of 51 distinct clades were observed, of which 21 clades are newly described. We further evaluated the delineation powers of the clade classification based on nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) retrieved from core-genome sequences; however, the delineation power of 8-HKGs is still high and that gene set can be reliably used for the classification and identification of Vibrionaceae. Furthermore, the 11-RPGs set proved to be useful in identifying uncultured species among metagenome-assembled genome (MAG) and/or single-cell genome-assembled genome (SAG) pools. This study expands the awareness of the diversity and evolutionary history of the family Vibrionaceae and accelerates the taxonomic applications in classifying as not-yet-cultured taxa among MAGs and SAGs.}, }
@article {pmid34904950, year = {2021}, author = {Ankersen, DV and Weimers, P and Bennedsen, M and Haaber, AB and Fjordside, EL and Beber, ME and Lieven, C and Saboori, S and Vad, N and Rannem, T and Marker, D and Paridaens, K and Frahm, S and Jensen, L and Rosager Hansen, M and Burisch, J and Munkholm, P}, title = {Long-Term Effects of a Web-Based Low-FODMAP Diet Versus Probiotic Treatment for Irritable Bowel Syndrome, Including Shotgun Analyses of Microbiota: Randomized, Double-Crossover Clinical Trial.}, journal = {Journal of medical Internet research}, volume = {23}, number = {12}, pages = {e30291}, doi = {10.2196/30291}, pmid = {34904950}, issn = {1438-8871}, abstract = {BACKGROUND: The long-term management of irritable bowel syndrome (IBS) poses many challenges. In short-term studies, eHealth interventions have been demonstrated to be safe and practical for at-home monitoring of the effects of probiotic treatments and a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs). IBS has been linked to alterations in the microbiota.<br><br>OBJECTIVE: The aim of this study was to determine whether a web-based low-FODMAP diet (LFD) intervention and probiotic treatment were equally good at reducing IBS symptoms, and whether the response to treatments could be explained by patients' microbiota.<br><br>METHODS: Adult IBS patients were enrolled in an open-label, randomized crossover trial (for nonresponders) with 1 year of follow-up using the web application IBS Constant Care (IBS CC). Patients were recruited from the outpatient clinic at the Department of Gastroenterology, North Zealand University Hospital, Denmark. Patients received either VSL#3 for 4 weeks (2 × 450 billion colony-forming units per day) or were placed on an LFD for 4 weeks. Patients responding to the LFD were reintroduced to foods high in FODMAPs, and probiotic responders received treatments whenever they experienced a flare-up of symptoms. Treatment response and symptom flare-ups were defined as a reduction or increase, respectively, of at least 50 points on the IBS Severity Scoring System (IBS-SSS). Web-based ward rounds were performed daily by the study investigator. Fecal microbiota were analyzed by shotgun metagenomic sequencing (at least 10 million 2 × 100 bp paired-end sequencing reads per sample).<br><br>RESULTS: A total of 34 IBS patients without comorbidities and 6 healthy controls were enrolled in the study. Taken from participating subjects, 180 fecal samples were analyzed for their microbiota composition. Out of 21 IBS patients, 12 (57%) responded to the LFD and 8 (38%) completed the reintroduction of FODMAPs. Out of 21 patients, 13 (62%) responded to their first treatment of VSL#3 and 7 (33%) responded to multiple VSL#3 treatments. A median of 3 (IQR 2.25-3.75) probiotic treatments were needed for sustained symptom control. LFD responders were reintroduced to a median of 14.50 (IQR 7.25-21.75) high-FODMAP items. No significant difference in the median reduction of IBS-SSS for LFD versus probiotic responders was observed, where for LFD it was -126.50 (IQR -196.75 to -76.75) and for VSL#3 it was -130.00 (IQR -211.00 to -70.50; P>.99). Responses to either of the two treatments were not able to be predicted using patients' microbiota.<br><br>CONCLUSIONS: The web-based LFD intervention and probiotic treatment were equally efficacious in managing IBS symptoms. The response to treatments could not be explained by the composition of the microbiota. The IBS CC web application was shown to be practical, safe, and useful for clinical decision making in the long-term management of IBS. Although this study was underpowered, findings from this study warrant further research in a larger sample of patients with IBS to confirm these long-term outcomes.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov NCT03586622; https://clinicaltrials.gov/ct2/show/NCT03586622.}, }
@article {pmid34904945, year = {2021}, author = {Rego, A and Fernandez-Guerra, A and Duarte, P and Assmy, P and Leão, PN and Magalhães, C}, title = {Secondary metabolite biosynthetic diversity in Arctic Ocean metagenomes.}, journal = {Microbial genomics}, volume = {7}, number = {12}, pages = {}, doi = {10.1099/mgen.0.000731}, pmid = {34904945}, issn = {2057-5858}, abstract = {Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are mega enzymes responsible for the biosynthesis of a large fraction of natural products (NPs). Molecular markers for biosynthetic genes, such as the ketosynthase (KS) domain of PKSs, have been used to assess the diversity and distribution of biosynthetic genes in complex microbial communities. More recently, metagenomic studies have complemented and enhanced this approach by allowing the recovery of complete biosynthetic gene clusters (BGCs) from environmental DNA. In this study, the distribution and diversity of biosynthetic genes and clusters from Arctic Ocean samples (NICE-2015 expedition), was assessed using PCR-based strategies coupled with high-throughput sequencing and metagenomic analysis. In total, 149 KS domain OTU sequences were recovered, 36 % of which could not be assigned to any known BGC. In addition, 74 bacterial metagenome-assembled genomes were recovered, from which 179 BGCs were extracted. A network analysis identified potential new NP families, including non-ribosomal peptides and polyketides. Complete or near-complete BGCs were recovered, which will enable future heterologous expression efforts to uncover the respective NPs. Our study represents the first report of biosynthetic diversity assessed for Arctic Ocean metagenomes and highlights the potential of Arctic Ocean planktonic microbiomes for the discovery of novel secondary metabolites. The strategy employed in this study will enable future bioprospection, by identifying promising samples for bacterial isolation efforts, while providing also full-length BGCs for heterologous expression.}, }
@article {pmid34904625, year = {2021}, author = {Zielezinski, A and Deorowicz, S and Gudyś, A}, title = {PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btab837}, pmid = {34904625}, issn = {1367-4811}, abstract = {SUMMARY: PHIST (Phage-Host Interaction Search Tool) predicts prokaryotic hosts of viruses based on exact matches between viral and host genomes. It improves host prediction accuracy at species level over current alignment-based tools (on average by 3 percentage points) as well as alignment-free and CRISPR-based tools (by 14-20 percentage points). PHIST is also two orders of magnitude faster than alignment-based tools making it suitable for metagenomics studies.<br><br>GNU-licensed C ++ code wrapped in Python API available at: https://github.com/refresh-bio/phist.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid34903850, year = {2021}, author = {Gregor, R and Probst, M and Eyal, S and Aksenov, A and Sasson, G and Horovitz, I and Dorrestein, PC and Meijler, MM and Mizrahi, I}, title = {Mammalian gut metabolomes mirror microbiome composition and host phylogeny.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {34903850}, issn = {1751-7370}, support = {640384//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 240356//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 1947/19//Israel Science Foundation (ISF)/ ; 1667/15//Israel Science Foundation (ISF)/ ; GMS10RR029121//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {In the past decade, studies on the mammalian gut microbiome have revealed that different animal species have distinct gut microbial compositions. The functional ramifications of this variation in microbial composition remain unclear: do these taxonomic differences indicate microbial adaptations to host-specific functionality, or are these diverse microbial communities essentially functionally redundant, as has been indicated by previous metagenomics studies? Here, we examine the metabolic content of mammalian gut microbiomes as a direct window into ecosystem function, using an untargeted metabolomics platform to analyze 101 fecal samples from a range of 25 exotic mammalian species in collaboration with a zoological center. We find that mammalian metabolomes are chemically diverse and strongly linked to microbiome composition, and that metabolome composition is further correlated to the phylogeny of the mammalian host. Specific metabolites enriched in different animal species included modified and degraded host and dietary compounds such as bile acids and triterpenoids, as well as fermentation products such as lactate and short-chain fatty acids. Our results suggest that differences in microbial taxonomic composition are indeed translated to host-specific metabolism, indicating that taxonomically distant microbiomes are more functionally diverse than redundant.}, }
@article {pmid34903237, year = {2021}, author = {Song, S and Ma, L and Xu, X and Shi, H and Li, X and Liu, Y and Hao, P}, title = {Rapid screening and identification of viral pathogens in metagenomic data.}, journal = {BMC medical genomics}, volume = {14}, number = {Suppl 6}, pages = {289}, pmid = {34903237}, issn = {1755-8794}, support = {XDB38030100//National Major Science and Technology Projects of China/ ; }, abstract = {BACKGROUND: Virus screening and viral genome reconstruction are urgent and crucial for the rapid identification of viral pathogens, i.e., tracing the source and understanding the pathogenesis when a viral outbreak occurs. Next-generation sequencing (NGS) provides an efficient and unbiased way to identify viral pathogens in host-associated and environmental samples without prior knowledge. Despite the availability of software, data analysis still requires human operations. A mature pipeline is urgently needed when thousands of viral pathogen and viral genome reconstruction samples need to be rapidly identified.<br><br>RESULTS: In this paper, we present a rapid and accurate workflow to screen metagenomics sequencing data for viral pathogens and other compositions, as well as enable a reference-based assembler to reconstruct viral genomes. Moreover, we tested our workflow on several metagenomics datasets, including a SARS-CoV-2 patient sample with NGS data, pangolins tissues with NGS data, Middle East Respiratory Syndrome (MERS)-infected cells with NGS data, etc. Our workflow demonstrated high accuracy and efficiency when identifying target viruses from large scale NGS metagenomics data. Our workflow was flexible when working with a broad range of NGS datasets from small (kb) to large (100 Gb). This took from a few minutes to a few hours to complete each task. At the same time, our workflow automatically generates reports that incorporate visualized feedback (e.g., metagenomics data quality statistics, host and viral sequence compositions, details about each of the identified viral pathogens and their coverages, and reassembled viral pathogen sequences based on their closest references).<br><br>CONCLUSIONS: Overall, our system enabled the rapid screening and identification of viral pathogens from metagenomics data, providing an important piece to support viral pathogen research during a pandemic. The visualized report contains information from raw sequence quality to a reconstructed viral sequence, which allows non-professional people to screen their samples for viruses by themselves (Additional file 1).}, }
@article {pmid34903050, year = {2021}, author = {Beller, L and Deboutte, W and Falony, G and Vieira-Silva, S and Tito, RY and Valles-Colomer, M and Rymenans, L and Jansen, D and Van Espen, L and Papadaki, MI and Shi, C and Yinda, CK and Zeller, M and Faust, K and Van Ranst, M and Raes, J and Matthijnssens, J}, title = {Successional Stages in Infant Gut Microbiota Maturation.}, journal = {mBio}, volume = {}, number = {}, pages = {e0185721}, doi = {10.1128/mBio.01857-21}, pmid = {34903050}, issn = {2150-7511}, abstract = {Disturbances in the primary colonization of the infant gut can result in lifelong consequences and have been associated with a range of host conditions. Although early-life factors have been shown to affect infant gut microbiota development, our current understanding of human gut colonization in early life remains limited. To gain more insights into the unique dynamics of this rapidly evolving ecosystem, we investigated the microbiota over the first year of life in eight densely sampled infants (n = 303 total samples). To evaluate the gut microbiota maturation transition toward an adult configuration, we compared the microbiome composition of the infants to that of the Flemish Gut Flora Project (FGFP) population (n = 1,106). We observed the infant gut microbiota to mature through three distinct, conserved stages of ecosystem development. Across these successional gut microbiota maturation stages, the genus predominance was observed to shift from Escherichia over Bifidobacterium to Bacteroides. Both disease and antibiotic treatment were observed to be associated occasionally with gut microbiota maturation stage regression, a transient setback in microbiota maturation dynamics. Although the studied microbiota trajectories evolved to more adult-like constellations, microbiome community typing against the background of the FGFP cohort clustered all infant samples within the (in adults) potentially dysbiotic Bacteroides 2 (Bact2) enterotype. We confirmed the similarities between infant gut microbial colonization and adult dysbiosis. Profound knowledge about the primary gut colonization process in infants might provide crucial insights into how the secondary colonization of a dysbiotic adult gut can be redirected. IMPORTANCE After birth, microbial colonization of the infant intestinal tract is important for health later in life. However, this initial process is highly dynamic and influenced by many factors. Studying this process in detail requires a dense longitudinal sampling effort. In the current study, the bacterial microbiota of >300 stool samples was analyzed from 8 healthy infants, suggesting that the infant gut microbial population matures along a path involving distinct microbial constellations and that the timing of these transitions is infant specific and can temporarily retrace upon external events. We also showed that the infant microbial populations show similarities to suboptimal bacterial populations in the guts of adults. These insights are crucial for a better understanding of the dynamics and characteristics of a "healthy gut microbial population" in both infants and adults and might allow the identification of intervention targets in cases of microbial disturbances or disease.}, }
@article {pmid34714829, year = {2021}, author = {Penev, PI and Alvarez-Carreño, C and Smith, E and Petrov, AS and Williams, LD}, title = {TwinCons: Conservation score for uncovering deep sequence similarity and divergence.}, journal = {PLoS computational biology}, volume = {17}, number = {10}, pages = {e1009541}, pmid = {34714829}, issn = {1553-7358}, support = {80NSSC18K1139/ImNASA/Intramural NASA/United States ; }, mesh = {Archaeal Proteins/chemistry/genetics ; Bacterial Proteins/chemistry/genetics ; Conserved Sequence/*genetics ; *Deep Learning ; Evolution, Molecular ; Metagenomics ; RNA, Ribosomal/*genetics ; Sequence Alignment/*methods ; Sequence Analysis, Protein/*methods ; }, abstract = {We have developed the program TwinCons, to detect noisy signals of deep ancestry of proteins or nucleic acids. As input, the program uses a composite alignment containing pre-defined groups, and mathematically determines a 'cost' of transforming one group to the other at each position of the alignment. The output distinguishes conserved, variable and signature positions. A signature is conserved within groups but differs between groups. The method automatically detects continuous characteristic stretches (segments) within alignments. TwinCons provides a convenient representation of conserved, variable and signature positions as a single score, enabling the structural mapping and visualization of these characteristics. Structure is more conserved than sequence. TwinCons highlights alternative sequences of conserved structures. Using TwinCons, we detected highly similar segments between proteins from the translation and transcription systems. TwinCons detects conserved residues within regions of high functional importance for the ribosomal RNA (rRNA) and demonstrates that signatures are not confined to specific regions but are distributed across the rRNA structure. The ability to evaluate both nucleic acid and protein alignments allows TwinCons to be used in combined sequence and structural analysis of signatures and conservation in rRNA and in ribosomal proteins (rProteins). TwinCons detects a strong sequence conservation signal between bacterial and archaeal rProteins related by circular permutation. This conserved sequence is structurally colocalized with conserved rRNA, indicated by TwinCons scores of rRNA alignments of bacterial and archaeal groups. This combined analysis revealed deep co-evolution of rRNA and rProtein buried within the deepest branching points in the tree of life.}, }
@article {pmid34521917, year = {2021}, author = {Leontidou, K and Vokou, D and Sandionigi, A and Bruno, A and Lazarina, M and De Groeve, J and Li, M and Varotto, C and Girardi, M and Casiraghi, M and Cristofori, A}, title = {Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18226}, pmid = {34521917}, issn = {2045-2322}, mesh = {*Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Genome, Plant ; Magnoliopsida/*classification/genetics/physiology ; Metagenome ; Metagenomics/*methods ; Pollen/*genetics ; }, abstract = {Monitoring biodiversity is of increasing importance in natural ecosystems. Metabarcoding can be used as a powerful molecular tool to complement traditional biodiversity monitoring, as total environmental DNA can be analyzed from complex samples containing DNA of different origin. The aim of this research was to demonstrate the potential of pollen DNA metabarcoding using the chloroplast trnL partial gene sequencing to characterize plant biodiversity. Collecting airborne biological particles with gravimetric Tauber traps in four Natura 2000 habitats within the Natural Park of Paneveggio Pale di San Martino (Italian Alps), at three-time intervals in 1 year, metabarcoding identified 68 taxa belonging to 32 local plant families. Metabarcoding could identify with finer taxonomic resolution almost all non-rare families found by conventional light microscopy concurrently applied. However, compared to microscopy quantitative results, Poaceae, Betulaceae, and Oleaceae were found to contribute to a lesser extent to the plant biodiversity and Pinaceae were more represented. Temporal changes detected by metabarcoding matched the features of each pollen season, as defined by aerobiological studies running in parallel, and spatial heterogeneity was revealed between sites. Our results showcase that pollen metabarcoding is a promising approach in detecting plant species composition which could provide support to continuous monitoring required in Natura 2000 habitats for biodiversity conservation.}, }
@article {pmid34508122, year = {2021}, author = {Suriyaphol, P and Chiu, JKH and Yimpring, N and Tunsagool, P and Mhuantong, W and Chuanchuen, R and Bessarab, I and Williams, RBH and Ong, RT and Suriyaphol, G}, title = {Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18091}, pmid = {34508122}, issn = {2045-2322}, mesh = {Age Factors ; Animals ; Anti-Bacterial Agents/*pharmacology ; Biodiversity ; Feces/*microbiology ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; Swine ; *Weaning ; }, abstract = {This study aimed to characterize the alteration of the fecal microbiome and antimicrobial resistance (AMR) determinants in 24 piglets at day 3 pre-weaning (D. - 3), weaning day (D.0), days 3 (D.3) and 8 post-weaning (D.8), using whole-genome shotgun sequencing. Distinct clusters of microbiomes and AMR determinants were observed at D.8 when Prevotella (20.9%) was the major genus, whereas at D. - 3-D.3, Alistipes (6.9-12.7%) and Bacteroides (5.2-8.5%) were the major genera. Lactobacillus and Escherichia were notably observed at D. - 3 (1.2%) and D. - 3-D.3 (0.2-0.4%), respectively. For AMR, a distinct cluster of AMR determinants was observed at D.8, mainly conferring resistance to macrolide-lincosamide-streptogramin (mefA), β-lactam (cfxA6 and aci1) and phenicol (rlmN). In contrast, at D. - 3-D.3, a high abundance of determinants with aminoglycoside (AMG) (sat, aac(6')-aph(2''), aadA and acrF), β-lactam (fus-1, cepA and mrdA), multidrug resistance (MDR) (gadW, mdtE, emrA, evgS, tolC and mdtB), phenicol (catB4 and cmlA4), and sulfonamide patterns (sul3) was observed. Canonical correlation analysis (CCA) plot associated Escherichia coli with aac(6')-aph(2''), emrA, mdtB, catB4 and cmlA4 at D. - 3, D.0 and/or D.3 whereas at D.8 associations between Prevotella and mefA, cfxA6 and aci1 were identified. The weaning age and diet factor played an important role in the microbial community composition.}, }
@article {pmid34504005, year = {2021}, author = {Büttner, H and Niehs, SP and Vandelannoote, K and Cseresnyés, Z and Dose, B and Richter, I and Gerst, R and Figge, MT and Stinear, TP and Pidot, SJ and Hertweck, C}, title = {Bacterial endosymbionts protect beneficial soil fungus from nematode attack.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {37}, pages = {}, pmid = {34504005}, issn = {1091-6490}, mesh = {Animals ; Anthelmintics/*pharmacology ; Burkholderiaceae/*physiology ; Genomics ; Lactones/*pharmacology ; Metabolic Networks and Pathways ; *Metagenome ; Mortierella/drug effects/*physiology ; Nematoda/*drug effects/pathogenicity ; Peptide Synthases/genetics/metabolism ; Phylogeny ; Soil Microbiology ; *Symbiosis ; }, abstract = {Fungi of the genus Mortierella occur ubiquitously in soils where they play pivotal roles in carbon cycling, xenobiont degradation, and promoting plant growth. These important fungi are, however, threatened by micropredators such as fungivorous nematodes, and yet little is known about their protective tactics. We report that Mortierella verticillata NRRL 6337 harbors a bacterial endosymbiont that efficiently shields its host from nematode attacks with anthelmintic metabolites. Microscopic investigation and 16S ribosomal DNA analysis revealed that a previously overlooked bacterial symbiont belonging to the genus Mycoavidus dwells in M. verticillata hyphae. Metabolic profiling of the wild-type fungus and a symbiont-free strain obtained by antibiotic treatment as well as genome analyses revealed that highly cytotoxic macrolactones (CJ-12,950 and CJ-13,357, syn necroxime C and D), initially thought to be metabolites of the soil-inhabiting fungus, are actually biosynthesized by the endosymbiont. According to comparative genomics, the symbiont belongs to a new species (Candidatus Mycoavidus necroximicus) with 12% of its 2.2 Mb genome dedicated to natural product biosynthesis, including the modular polyketide-nonribosomal peptide synthetase for necroxime assembly. Using Caenorhabditis elegans and the fungivorous nematode Aphelenchus avenae as test strains, we show that necroximes exert highly potent anthelmintic activities. Effective host protection was demonstrated in cocultures of nematodes with symbiotic and chemically complemented aposymbiotic fungal strains. Image analysis and mathematical quantification of nematode movement enabled evaluation of the potency. Our work describes a relevant role for endofungal bacteria in protecting fungi against mycophagous nematodes.}, }
@article {pmid34297922, year = {2021}, author = {Lee, JWJ and Plichta, D and Hogstrom, L and Borren, NZ and Lau, H and Gregory, SM and Tan, W and Khalili, H and Clish, C and Vlamakis, H and Xavier, RJ and Ananthakrishnan, AN}, title = {Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease.}, journal = {Cell host &amp; microbe}, volume = {29}, number = {8}, pages = {1294-1304.e4}, pmid = {34297922}, issn = {1934-6069}, support = {R01 AT009708/AT/NCCIH NIH HHS/United States ; U19 AI110495/AI/NIAID NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R21 DK127227/DK/NIDDK NIH HHS/United States ; U19 AI142784/AI/NIAID NIH HHS/United States ; }, mesh = {Antibodies, Monoclonal, Humanized ; *Biological Therapy ; Biomarkers ; Blood ; Colitis, Ulcerative/*therapy ; Crohn Disease/therapy ; Cytokines/blood/drug effects ; Feces ; Gastrointestinal Microbiome/*physiology ; Humans ; *Inflammatory Bowel Diseases/microbiology/therapy ; Infliximab ; Metabolomics ; Metagenome ; Prospective Studies ; Proteomics ; Tumor Necrosis Factor Inhibitors/therapeutic use ; }, abstract = {The intestinal microbiome is a key determinant of responses to biologic therapy in inflammatory bowel disease (IBD). However, diverse therapeutics and variable responses among IBD patients have posed challenges in predicting clinical therapeutic success. In this prospective study, we profiled baseline stool and blood in patients with moderate-to-severe Crohn's disease or ulcerative colitis initiating anti-cytokine therapy (anti-TNF or -IL12/23) or anti-integrin therapy. Patients were assessed at 14 weeks for clinical remission and 52 weeks for clinical and endoscopic remission. Baseline microbial richness indicated preferential responses to anti-cytokine therapy and correlated with the abundance of microbial species capable of 7α/β-dehydroxylation of primary to secondary bile acids. Serum signatures of immune proteins reflecting microbial diversity identified patients more likely to achieve remission with anti-cytokine therapy. Remission-associated multi-omic profiles were unique to each therapeutic class. These profiles may facilitate a priori determination of optimal therapeutics for patients and serve as targets for newer therapies.}, }
@article {pmid34289377, year = {2021}, author = {Zhang, XS and Yin, YS and Wang, J and Battaglia, T and Krautkramer, K and Li, WV and Li, J and Brown, M and Zhang, M and Badri, MH and Armstrong, AJS and Strauch, CM and Wang, Z and Nemet, I and Altomare, N and Devlin, JC and He, L and Morton, JT and Chalk, JA and Needles, K and Liao, V and Mount, J and Li, H and Ruggles, KV and Bonneau, RA and Dominguez-Bello, MG and Bäckhed, F and Hazen, SL and Blaser, MJ}, title = {Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice.}, journal = {Cell host &amp; microbe}, volume = {29}, number = {8}, pages = {1249-1265.e9}, pmid = {34289377}, issn = {1934-6069}, support = {R01 DK110014/DK/NIDDK NIH HHS/United States ; R01 DK120679/DK/NIDDK NIH HHS/United States ; R01 GM128955/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Autoimmune Diseases ; Bacteria/classification/drug effects ; Cecum/*immunology/*microbiology ; Diabetes Mellitus, Type 1/*immunology ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*drug effects/*physiology ; Gene Expression ; Histone Code ; Intestines/immunology ; Male ; Metabolic Networks and Pathways ; Metagenome ; Mice ; Mice, Inbred NOD ; MicroRNAs ; }, abstract = {Early-life antibiotic exposure perturbs the intestinal microbiota and accelerates type 1 diabetes (T1D) development in the NOD mouse model. Here, we found that maternal cecal microbiota transfer (CMT) to NOD mice after early-life antibiotic perturbation largely rescued the induced T1D enhancement. Restoration of the intestinal microbiome was significant and persistent, remediating the antibiotic-depleted diversity, relative abundance of particular taxa, and metabolic pathways. CMT also protected against perturbed metabolites and normalized innate and adaptive immune effectors. CMT restored major patterns of ileal microRNA and histone regulation of gene expression. Further experiments suggest a gut-microbiota-regulated T1D protection mechanism centered on Reg3γ, in an innate intestinal immune network involving CD44, TLR2, and Reg3γ. This regulation affects downstream immunological tone, which may lead to protection against tissue-specific T1D injury.}, }
@article {pmid34253790, year = {2021}, author = {Sawaswong, V and Praianantathavorn, K and Chanchaem, P and Khamwut, A and Kemthong, T and Hamada, Y and Malaivijitnond, S and Payungporn, S}, title = {Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {14280}, pmid = {34253790}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; Body Weight ; Ecosystem ; Female ; Firmicutes/*metabolism ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Macaca/*microbiology/*physiology ; Male ; Metagenomics ; Microbiota ; Mouth Mucosa/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Thailand ; Zoology ; }, abstract = {Long-tailed macaques (Macaca fascicularis), distributed in Southeast Asia, are generally used in biomedical research. At present, the expansion of human communities overlapping of macaques' natural habitat causes human-macaque conflicts. To mitigate this problem in Thailand, the National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU), was granted the permit to catch the surplus wild-born macaques and transfer them to the center. Based on the fact that the diets provided and the captive environments were different, their oral-gut microbiota should be altered. Thus, we investigated and compared the oral and fecal microbiome between wild-born macaques that lived in the natural habitats and those transferred to and reared in the NPRCT-CU for 1 year. The results from 16S rRNA high-throughput sequencing showed that the captive macaques had distinct oral-gut microbiota profiles and lower bacterial richness compared to those in wild macaques. The gut of wild macaques was dominated by Firmicutes which is probably associated with lipid absorption and storage. These results implicated the effects of captivity conditions on the microbiome that might contribute to crucial metabolic functions. Our study should be applied to the animal health care program, with respect to microbial functions, for non-human primates.}, }
@article {pmid34207804, year = {2021}, author = {Hardouin, P and Chiron, R and Marchandin, H and Armengaud, J and Grenga, L}, title = {Metaproteomics to Decipher CF Host-Microbiota Interactions: Overview, Challenges and Future Perspectives.}, journal = {Genes}, volume = {12}, number = {6}, pages = {}, pmid = {34207804}, issn = {2073-4425}, mesh = {Animals ; Cystic Fibrosis/metabolism/*microbiology ; *Host-Pathogen Interactions ; Humans ; Metagenomics/*methods ; *Microbiota ; Proteome/genetics/metabolism ; Proteomics/*methods ; }, abstract = {Cystic fibrosis (CF) is a hereditary disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, triggering dysfunction of the anion channel in several organs including the lung and gut. The main cause of morbidity and mortality is chronic infection. The microbiota is now included among the additional factors that could contribute to the exacerbation of patient symptoms, to treatment outcome, and more generally to the phenotypic variability observed in CF patients. In recent years, various omics tools have started to shed new light on microbial communities associated with CF and host-microbiota interactions. In this context, proteomics targets the key effectors of the responses from organisms, and thus their phenotypes. Recent advances are promising in terms of gaining insights into the CF microbiota and its relation with the host. This review provides an overview of the contributions made by proteomics and metaproteomics to our knowledge of the complex host-microbiota partnership in CF. Considering the strengths and weaknesses of proteomics-based approaches in profiling the microbiota in the context of other diseases, we illustrate their potential and discuss possible strategies to overcome their limitations in monitoring both the respiratory and intestinal microbiota in sample from patients with CF.}, }
@article {pmid34201311, year = {2021}, author = {Šulčius, S and Alzbutas, G and Juknevičiūtė, V and Šimoliūnas, E and Venckus, P and Šimoliūnienė, M and Paškauskas, R}, title = {Exploring Viral Diversity in a Gypsum Karst Lake Ecosystem Using Targeted Single-Cell Genomics.}, journal = {Genes}, volume = {12}, number = {6}, pages = {}, pmid = {34201311}, issn = {2073-4425}, mesh = {Bacterial Proteins/genetics/metabolism ; Bacteriophages/*genetics/isolation &amp; purification/pathogenicity ; Calcium Sulfate/analysis/metabolism ; Chlorobium/genetics/metabolism/*virology ; Genomics/methods ; Host-Pathogen Interactions ; Lakes/chemistry/*microbiology/virology ; Metagenome ; Single-Cell Analysis/methods ; Sulfur/metabolism ; *Virome ; }, abstract = {Little is known about the diversity and distribution of viruses infecting green sulfur bacteria (GSB) thriving in euxinic (sulfuric and anoxic) habitats, including gypsum karst lake ecosystems. In this study, we used targeted cell sorting combined with single-cell sequencing to gain insights into the gene content and genomic potential of viruses infecting sulfur-oxidizing bacteria Chlorobium clathratiforme, obtained from water samples collected during summer stratification in gypsum karst Lake Kirkilai (Lithuania). In total, 82 viral contigs were bioinformatically identified in 62 single amplified genomes (SAGs) of C. clathratiforme. The majority of viral gene and protein sequences showed little to no similarity with phage sequences in public databases, uncovering the vast diversity of previously undescribed GSB viruses. We observed a high level of lysogenization in the C. clathratiforme population, as 87% SAGs contained intact prophages. Among the thirty identified auxiliary metabolic genes (AMGs), two, thiosulfate sulfurtransferase (TST) and thioredoxin-dependent phosphoadenosine phosphosulfate (PAPS) reductase (cysH), were found to be involved in the oxidation of inorganic sulfur compounds, suggesting that viruses can influence the metabolism and cycling of this essential element. Finally, the analysis of CRISPR spacers retrieved from the consensus C. clathratiforme genome imply persistent and active virus-host interactions for several putative phages prevalent among C. clathratiforme SAGs. Overall, this study provides a glimpse into the diversity of phages associated with naturally occurring and highly abundant sulfur-oxidizing bacteria.}, }
@article {pmid34172012, year = {2021}, author = {Lay, C and Chu, CW and Purbojati, RW and Acerbi, E and Drautz-Moses, DI and de Sessions, PF and Jie, S and Ho, E and Kok, YJ and Bi, X and Chen, S and Mak, SY and Chua, MC and Goh, AEN and Chiang, WC and Rao, R and Chaithongwongwatthana, S and Khemapech, N and Chongsrisawat, V and Martin, R and ,  and Roeselers, G and Ho, YS and Hibberd, ML and Schuster, SC and Knol, J}, title = {A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {191}, pmid = {34172012}, issn = {1471-2180}, mesh = {Bacteria/*genetics ; Biodiversity ; Cesarean Section/*adverse effects ; Double-Blind Method ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant ; Infant, Newborn ; Metagenome/*genetics ; }, abstract = {BACKGROUND: The compromised gut microbiome that results from C-section birth has been hypothesized as a risk factor for the development of non-communicable diseases (NCD). In a double-blind randomized controlled study, 153 infants born by elective C-section received an infant formula supplemented with either synbiotic, prebiotics, or unsupplemented from birth until 4 months old. Vaginally born infants were included as a reference group. Stool samples were collected from day 3 till week 22. Multi-omics were deployed to investigate the impact of mode of delivery and nutrition on the development of the infant gut microbiome, and uncover putative biological mechanisms underlying the role of a compromised microbiome as a risk factor for NCD.<br><br>RESULTS: As early as day 3, infants born vaginally presented a hypoxic and acidic gut environment characterized by an enrichment of strict anaerobes (Bifidobacteriaceae). Infants born by C-section presented the hallmark of a compromised microbiome driven by an enrichment of Enterobacteriaceae. This was associated with meta-omics signatures characteristic of a microbiome adapted to a more oxygen-rich gut environment, enriched with genes associated with reactive oxygen species metabolism and lipopolysaccharide biosynthesis, and depleted in genes involved in the metabolism of milk carbohydrates. The synbiotic formula modulated expression of microbial genes involved in (oligo)saccharide metabolism, which emulates the eco-physiological gut environment observed in vaginally born infants. The resulting hypoxic and acidic milieu prevented the establishment of a compromised microbiome.<br><br>CONCLUSIONS: This study deciphers the putative functional hallmarks of a compromised microbiome acquired during C-section birth, and the impact of nutrition that may counteract disturbed microbiome development.<br><br>TRIAL REGISTRATION: The study was registered in the Dutch Trial Register (Number: 2838) on 4th April 2011.}, }
@article {pmid34155108, year = {2021}, author = {Burke, EJ and Rodda, SS and Lund, SR and Sun, Z and Zeroka, MR and O'Toole, KH and Parker, MJ and Doshi, DS and Guan, C and Lee, YJ and Dai, N and Hough, DM and Shnider, DA and Corrêa, IR and Weigele, PR and Saleh, L}, title = {Phage-encoded ten-eleven translocation dioxygenase (TET) is active in C5-cytosine hypermodification in DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {26}, pages = {}, pmid = {34155108}, issn = {1091-6490}, mesh = {5-Methylcytosine/*metabolism ; Amino Acid Sequence ; Bacteriophages/*metabolism ; DNA/*metabolism ; DNA Methylation ; Dioxygenases ; Hydroxylation ; Metagenomics ; Nucleotide Motifs/genetics ; Oxidation-Reduction ; Phylogeny ; }, abstract = {TET/JBP (ten-eleven translocation/base J binding protein) enzymes are iron(II)- and 2-oxo-glutarate-dependent dioxygenases that are found in all kingdoms of life and oxidize 5-methylpyrimidines on the polynucleotide level. Despite their prevalence, few examples have been biochemically characterized. Among those studied are the metazoan TET enzymes that oxidize 5-methylcytosine in DNA to hydroxy, formyl, and carboxy forms and the euglenozoa JBP dioxygenases that oxidize thymine in the first step of base J biosynthesis. Both enzymes have roles in epigenetic regulation. It has been hypothesized that all TET/JBPs have their ancestral origins in bacteriophages, but only eukaryotic orthologs have been described. Here we demonstrate the 5mC-dioxygenase activity of several phage TETs encoded within viral metagenomes. The clustering of these TETs in a phylogenetic tree correlates with the sequence specificity of their genomically cooccurring cytosine C5-methyltransferases, which install the methyl groups upon which TETs operate. The phage TETs favor Gp5mC dinucleotides over the 5mCpG sites targeted by the eukaryotic TETs and are found within gene clusters specifying complex cytosine modifications that may be important for DNA packaging and evasion of host restriction.}, }
@article {pmid34132943, year = {2021}, author = {Luo, R and Zhang, X and Wang, L and Zhang, L and Li, G and Zheng, Z}, title = {GLIS1, a potential candidate gene affect fat deposition in sheep tail.}, journal = {Molecular biology reports}, volume = {48}, number = {5}, pages = {4925-4931}, pmid = {34132943}, issn = {1573-4978}, support = {ZDZX2018065//Science and Technology Major Project of Inner Mongolia Autonomous Region of China/ ; }, mesh = {Animals ; China ; Genomics ; Lipid Metabolism/*genetics ; Metagenomics ; Mutation ; Platelet-Derived Growth Factor/genetics/metabolism ; Polymorphism, Single Nucleotide ; *Sheep, Domestic/genetics/metabolism ; Tail/*metabolism ; Transcription Factors/genetics/metabolism ; Whole Genome Sequencing ; Zinc Fingers/*genetics ; }, abstract = {Fat deposition in sheep tails is as a result of a complicated mechanism. Mongolian sheep (MG) and Small Tail Han sheep (STH) are two fat-tailed Chinese indigenous sheep breeds while DairyMeade and East Friesian (DS) are two thin-tailed dairy sheep breeds recently introduced to China. In this study, population genomics analysis was applied to identify candidate genes associated with sheep tails based on an in-depth whole-genome sequencing of MG, STH and DS. The selective signature analysis demonstrated that GLIS1, LOC101117953, PDGFD and T were in the significant divergent regions between DS and STH-MG. A nonsynonymous point mutation (g.27807636G>T) was found within GLIS1 in STH-MG and resulted in a Pro to Thr substitution. As a pro-adipogenic factor, GLIS1 may play critical roles in the mesodermal cell differentiation during fetal development affecting fat deposition in sheep tails. This study gives a new insight into the genetic basis of species-specific traits of sheep tails.}, }
@article {pmid34016748, year = {2021}, author = {Drott, MT and Rush, TA and Satterlee, TR and Giannone, RJ and Abraham, PE and Greco, C and Venkatesh, N and Skerker, JM and Glass, NL and Labbé, JL and Milgroom, MG and Keller, NP}, title = {Microevolution in the pansecondary metabolome of Aspergillus flavus and its potential macroevolutionary implications for filamentous fungi.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {21}, pages = {}, pmid = {34016748}, issn = {1091-6490}, mesh = {Aspergillus/classification/genetics/*metabolism ; Aspergillus flavus/classification/genetics/*metabolism ; Fungal Proteins/genetics/metabolism ; Genetic Speciation ; *Genome, Fungal ; Genomics ; *Metabolome ; Metagenomics ; Multigene Family ; Phylogeny ; Secondary Metabolism/*genetics ; United States ; }, abstract = {Fungi produce a wealth of pharmacologically bioactive secondary metabolites (SMs) from biosynthetic gene clusters (BGCs). It is common practice for drug discovery efforts to treat species' secondary metabolomes as being well represented by a single or a small number of representative genomes. However, this approach misses the possibility that intraspecific population dynamics, such as adaptation to environmental conditions or local microbiomes, may harbor novel BGCs that contribute to the overall niche breadth of species. Using 94 isolates of Aspergillus flavus, a cosmopolitan model fungus, sampled from seven states in the United States, we dereplicate 7,821 BGCs into 92 unique BGCs. We find that more than 25% of pangenomic BGCs show population-specific patterns of presence/absence or protein divergence. Population-specific BGCs make up most of the accessory-genome BGCs, suggesting that different ecological forces that maintain accessory genomes may be partially mediated by population-specific differences in secondary metabolism. We use ultra-high-performance high-resolution mass spectrometry to confirm that these genetic differences in BGCs also result in chemotypic differences in SM production in different populations, which could mediate ecological interactions and be acted on by selection. Thus, our results suggest a paradigm shift that previously unrealized population-level reservoirs of SM diversity may be of significant evolutionary, ecological, and pharmacological importance. Last, we find that several population-specific BGCs from A. flavus are present in Aspergillus parasiticus and Aspergillus minisclerotigenes and discuss how the microevolutionary patterns we uncover inform macroevolutionary inferences and help to align fungal secondary metabolism with existing evolutionary theory.}, }
@article {pmid33972424, year = {2021}, author = {Fellows Yates, JA and Velsko, IM and Aron, F and Posth, C and Hofman, CA and Austin, RM and Parker, CE and Mann, AE and Nägele, K and Arthur, KW and Arthur, JW and Bauer, CC and Crevecoeur, I and Cupillard, C and Curtis, MC and Dalén, L and Díaz-Zorita Bonilla, M and Díez Fernández-Lomana, JC and Drucker, DG and Escribano Escrivá, E and Francken, M and Gibbon, VE and González Morales, MR and Grande Mateu, A and Harvati, K and Henry, AG and Humphrey, L and Menéndez, M and Mihailović, D and Peresani, M and Rodríguez Moroder, S and Roksandic, M and Rougier, H and Sázelová, S and Stock, JT and Straus, LG and Svoboda, J and Teßmann, B and Walker, MJ and Power, RC and Lewis, CM and Sankaranarayanan, K and Guschanski, K and Wrangham, RW and Dewhirst, FE and Salazar-García, DC and Krause, J and Herbig, A and Warinner, C}, title = {The evolution and changing ecology of the African hominid oral microbiome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {20}, pages = {}, pmid = {33972424}, issn = {1091-6490}, support = {R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 GM089886/GM/NIGMS NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Africa ; Animals ; Bacteria/classification/genetics ; Biofilms ; *Biological Evolution ; Dental Plaque/microbiology ; Ecology/*methods ; Geography ; Gorilla gorilla/microbiology ; Hominidae/classification/*microbiology ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; Mouth/*microbiology ; Pan troglodytes/microbiology ; Phylogeny ; }, abstract = {The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.}, }
@article {pmid33856965, year = {2021}, author = {Davidson, RM and Hasan, NA and Epperson, LE and Benoit, JB and Kammlade, SM and Levin, AR and Calado de Moura, V and Hunkins, J and Weakly, N and Beagle, S and Sagel, SD and Martiniano, SL and Salfinger, M and Daley, CL and Nick, JA and Strong, M}, title = {Population Genomics of Mycobacterium abscessus from U.S. Cystic Fibrosis Care Centers.}, journal = {Annals of the American Thoracic Society}, volume = {18}, number = {12}, pages = {1960-1969}, pmid = {33856965}, issn = {2325-6621}, support = {K01 AI125726/AI/NIAID NIH HHS/United States ; R01 HL146228/HL/NHLBI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; *Cystic Fibrosis/epidemiology ; Genomics ; Humans ; Metagenomics ; Microbial Sensitivity Tests ; *Mycobacterium Infections, Nontuberculous/epidemiology ; *Mycobacterium abscessus/genetics ; United States/epidemiology ; }, abstract = {Rationale: Mycobacterium abscessus is a significant threat to individuals with cystic fibrosis (CF) because of innate drug resistance and potential transmission between patients. Recent studies described global dominant circulating clones of M. abscessus, but detailed genomic surveys have not yet been described for the United States. Objectives: We examined the genetic diversity of respiratory M. abscessus isolates from U.S. patients with CF and evaluated the potential for transmission events within CF Care Centers. Methods: Whole-genome sequencing was performed on 558 M. abscessus isolates from 266 patients with CF attending 48 CF Care Centers in 28 U.S. states as part of a nationwide surveillance program. U.S. isolates were also compared with 64 isolate genomes from 13 previous studies to evaluate the prevalence of recently described dominant circulating clones. Results: More than half of study patients with CF and M. abscessus had isolates within four dominant clones; two clones of M. abscessus subspecies (subsp.) abscessus (MAB) and two clones of M. abscessus subsp. massiliense (MMAS). Acquired drug resistance mutations for aminoglycosides and macrolides were rare in the isolate population, and they were not significantly enriched in dominant clones compared with unclustered isolates. For a subset of 55 patients, there was no relationship between dominant clones and diagnosis of active lung disease (P = 1.0). Twenty-nine clusters of genetically similar MAB isolates and eight clusters of genetically similar MMAS isolates were identified. Overall, 28 of 204 (14%) patients with MAB and 15 of 64 (23%) patients with MMAS had genetically isolates similar to those of at least one other patient at the same CF Care Center. Genetically similar isolates were also found between 60 of 204 (29%) patients with MAB and 19 of 64 (30%) patients with MMAS from different geographic locations. Conclusions: Our study reveals the predominant genotypes of M. abscessus and frequency of shared strains between patients in U.S. CF Care Centers. Integrated epidemiological and environmental studies would help to explain the widespread presence of dominant clones in the United States, including the potential for broad distribution in the environment. Single site studies using systematic, evidence-based approaches will be needed to establish the contributions of health care-associated transmission versus shared environmental exposures.}, }
@article {pmid33723291, year = {2021}, author = {Desbois, AC and Ciocan, D and Saadoun, D and Perlemuter, G and Cacoub, P}, title = {Specific microbiome profile in Takayasu's arteritis and giant cell arteritis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5926}, pmid = {33723291}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Biomarkers/blood ; Computational Biology/methods ; *Disease Susceptibility ; Female ; Giant Cell Arteritis/drug therapy/*etiology/metabolism/pathology ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Sepsis/complications/microbiology ; Takayasu Arteritis/drug therapy/*etiology/metabolism/pathology ; }, abstract = {Recent studies have provided evidence of a close link between specific microbiota and inflammatory disorders. While the vessel wall microbiota has been recently described in large vessel vasculitis (LVV) and controls, the blood microbiome in these diseases has not been previously reported (LVV). We aimed to analyse the blood microbiome profile of LVV patients (Takayasu's arteritis [TAK], giant cell arteritis [GCA]) and healthy blood donors (HD). We studied the blood samples of 13 patients with TAK (20 samples), 9 patients with GCA (11 samples) and 15 HD patients. We assessed the blood microbiome profile by sequencing the 16S rDNA blood bacterial DNA. We used linear discriminant analysis (LDA) coupled with linear discriminant effect size measurement (LEfSe) to investigate the differences in the blood microbiome profile between TAK and GCA patients. An increase in the levels of Clostridia, Cytophagia and Deltaproteobacteria and a decrease in Bacilli at the class level were found in TAK patients compared with HD patients (LDA > 2, p < 0.05). Active TAK patients had significantly lower levels of Staphylococcus compared with inactive TAK patients. Samples of GCA patients had an increased abundance of Rhodococcus and an unidentified member of the Cytophagaceae family. Microbiota of TAK compared with GCA patients was found to show higher levels of Candidatus Aquiluna and Cloacibacterium (LDA > 2; p < 0.05). Differences highlighted in the blood microbiome were also associated with a shift of bacterial predicted metabolic functions in TAK in comparison with HD. Similar results were also found in patients with active versus inactive TAK. In conclusion, patients with TAK were found to present a specific blood microbiome profile in comparison with healthy donors and GCA subjects. Significant changes in the blood microbiome profiles of TAK patients were associated with specific metabolic functions.}, }
@article {pmid33723271, year = {2021}, author = {Papa, G and Di Prisco, G and Spini, G and Puglisi, E and Negri, I}, title = {Acute and chronic effects of Titanium dioxide (TiO2) PM1 on honey bee gut microbiota under laboratory conditions.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5946}, pmid = {33723271}, issn = {2045-2322}, mesh = {Animals ; *Bees ; Biodiversity ; Environmental Pollutants/*adverse effects ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Particulate Matter/*adverse effects ; Titanium/*adverse effects/chemistry ; }, abstract = {Apis mellifera is an important provider of ecosystem services, and during flight and foraging behaviour is exposed to environmental pollutants including airborne particulate matter (PM). While exposure to insecticides, antibiotics, and herbicides may compromise bee health through alterations of the gut microbial community, no data are available on the impacts of PM on the bee microbiota. Here we tested the effects of ultrapure Titanium dioxide (TiO2) submicrometric PM (i.e., PM1, less than 1 µm in diameter) on the gut microbiota of adult bees. TiO2 PM1 is widely used as a filler and whitening agent in a range of manufactured objects, and ultrapure TiO2 PM1 is also a common food additive, even if it has been classified by the International Agency for Research on Cancer (IARC) as a possible human carcinogen in Group 2B. Due to its ubiquitous use, honey bees may be severely exposed to TiO2 ingestion through contaminated honey and pollen. Here, we demonstrated that acute and chronic oral administration of ultrapure TiO2 PM1 to adult bees alters the bee microbial community; therefore, airborne PM may represent a further risk factor for the honey bee health, promoting sublethal effects against the gut microbiota.}, }
@article {pmid33633264, year = {2021}, author = {Staley, C and Halaweish, H and Graiziger, C and Hamilton, MJ and Kabage, AJ and Galdys, AL and Vaughn, BP and Vantanasiri, K and Suryanarayanan, R and Sadowsky, MJ and Khoruts, A}, title = {Lower endoscopic delivery of freeze-dried intestinal microbiota results in more rapid and efficient engraftment than oral administration.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4519}, pmid = {33633264}, issn = {2045-2322}, mesh = {Aged ; Aged, 80 and over ; Biodiversity ; Clostridium Infections/*microbiology/*therapy ; Disease Management ; Disease Susceptibility ; Fecal Microbiota Transplantation/*methods ; Female ; Freeze Drying ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Transanal Endoscopic Microsurgery/*methods ; Treatment Outcome ; }, abstract = {Fecal microbiota transplantation (FMT) is a highly effective treatment for recurrent Clostridioides difficile infection (rCDI). However, standardization of FMT products is essential for its broad implementation into clinical practice. We have developed an oral preparation of freeze-dried, encapsulated microbiota, which is ~ 80% clinically effective, but results in delayed engraftment of donor bacteria relative to administration via colonoscopy. Our objective was to measure the engraftment potential of freeze-dried microbiota without the complexity of variables associated with oral administration. We compared engraftment of identical preparations and doses of freeze-dried microbiota following colonoscopic (9 patients) versus oral administration (18 patients). Microbiota were characterized by sequencing of the 16S rRNA gene, and engraftment was determined using the SourceTracker algorithm. Oligotyping analysis was done to provide high-resolution patterns of microbiota engraftment. Colonoscopic FMT was associated with greater levels of donor engraftment within days following the procedure (ANOVA P = 0.035) and specific increases in the relative abundances of donor Lachnospiraceae, Bacteroidaceae, and Porphyromonadaceae (P ≤ 0.033). Lower relative abundances of Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae families were associated with clinical failures. These results suggest that further optimization of oral capsule FMT may improve its engraftment efficiency and clinical efficacy.}, }
@article {pmid33633172, year = {2021}, author = {Carrieri, AP and Haiminen, N and Maudsley-Barton, S and Gardiner, LJ and Murphy, B and Mayes, AE and Paterson, S and Grimshaw, S and Winn, M and Shand, C and Hadjidoukas, P and Rowe, WPM and Hawkins, S and MacGuire-Flanagan, A and Tazzioli, J and Kenny, JG and Parida, L and Hoptroff, M and Pyzer-Knapp, EO}, title = {Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4565}, pmid = {33633172}, issn = {2045-2322}, mesh = {Adult ; Aged ; Aging ; *Artificial Intelligence ; *Biodiversity ; Computational Biology/methods ; Data Analysis ; Deep Learning ; Female ; Humans ; Male ; Menopause ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; *Phenotype ; Skin/*microbiology ; Smokers ; Young Adult ; }, abstract = {Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets can offer an improved understanding of the microbiome's role in human health. To gain actionable insights it is essential to consider both the predictive power and the transparency of the models by providing explanations for the predictions. We combine the collection of leg skin microbiome samples from two healthy cohorts of women with the application of an explainable artificial intelligence (EAI) approach that provides accurate predictions of phenotypes with explanations. The explanations are expressed in terms of variations in the relative abundance of key microbes that drive the predictions. We predict skin hydration, subject's age, pre/post-menopausal status and smoking status from the leg skin microbiome. The changes in microbial composition linked to skin hydration can accelerate the development of personalized treatments for healthy skin, while those associated with age may offer insights into the skin aging process. The leg microbiome signatures associated with smoking and menopausal status are consistent with previous findings from oral/respiratory tract microbiomes and vaginal/gut microbiomes respectively. This suggests that easily accessible microbiome samples could be used to investigate health-related phenotypes, offering potential for non-invasive diagnosis and condition monitoring. Our EAI approach sets the stage for new work focused on understanding the complex relationships between microbial communities and phenotypes. Our approach can be applied to predict any condition from microbiome samples and has the potential to accelerate the development of microbiome-based personalized therapeutics and non-invasive diagnostics.}, }
@article {pmid33624402, year = {2021}, author = {Wang, Y and Paterson, AH}, title = {Loquat (Eriobotrya japonica (Thunb.) Lindl) population genomics suggests a two-staged domestication and identifies genes showing convergence/parallel selective sweeps with apple or peach.}, journal = {The Plant journal : for cell and molecular biology}, volume = {106}, number = {4}, pages = {942-952}, doi = {10.1111/tpj.15209}, pmid = {33624402}, issn = {1365-313X}, mesh = {Crops, Agricultural ; Domestication ; Eriobotrya/*genetics ; Genome, Plant/*genetics ; Malus/*genetics ; *Metagenomics ; Phylogeny ; Plant Breeding ; Polymorphism, Genetic/*genetics ; Prunus persica/*genetics ; }, abstract = {Crop domestication and evolution represent key fields of plant and genetics research. Here, we re-sequenced and analyzed whole genome data from 51 wild accessions and 53 representative cultivars of Eriobotrya japonica, an important semi-subtropical fruit crop. Population genomics analysis suggested that modern cultivated E. japonica experienced a two-staged domestication fitting the "marginality model," being initially domesticated in west-northern Hubei province from a mono-phylogenetic wild progenitor, then refined mainly in Jiangsu, Zhejiang and Fujian provinces of China. Cultivated E. japonica has experienced little reduction in genome-wide nucleotide polymorphism compared with wild forms. Genes responsible for sugar biosynthesis were enriched in regions harboring putative selective sweeps. An approach based on co-clustering into gene families and evaluating chromosome colinearity of orthologous and paralogous genes was used to identify convergent/parallel selective sweeps among different crops. Specifically, more than one hundred of orthologs and paralogs undergoing selective sweeps were identified between loquat, apple and peach, among which 14 encoded "UDP glycosyltransferase 1." In sum, the study not only provided valuable information for breeding of E. japonica, but also enriched knowledge of crop domestication.}, }
@article {pmid33619300, year = {2021}, author = {Reed, KJ and Kunz, IGZ and Scare, JA and Nielsen, MK and Turk, PJ and Coleman, RJ and Coleman, SJ}, title = {The pelvic flexure separates distinct microbial communities in the equine hindgut.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4332}, pmid = {33619300}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; *Gastrointestinal Microbiome ; *Horses ; *Intestine, Large ; Metagenome ; Metagenomics/methods ; Pelvis/*anatomy &amp; histology ; }, abstract = {As hindgut fermenters, horses are especially dependent on the microbiota residing in their cecum and large intestines. Interactions between these microbial populations and the horse are critical for maintaining gut homeostasis, which supports proper digestion. The current project was motivated to determine if any features of the fecal microbiota are informative of the microbial communities from the cecum, ventral colon, or dorsal colon. Digesta from the cecum, ventral colon, dorsal colon and feces were collected from 6 yearling miniature horses. Microbial DNA was isolated and the microbiota from each sample was characterized by profiling the V4 region of the 16S rRNA. Principal coordinate analysis of the beta diversity results revealed significant (p = 0.0001; F = 5.2393) similarities between the microbial populations from cecal and ventral colon and the dorsal colon and fecal samples, however, there was little overlap between the proximal and distal ends of the hindgut. These distinct population structures observed in our results coincide with the pelvic flexure, which itself separates intestinal compartments with distinct roles in digestive physiology. An indicator species analysis confirmed the population differences, supported by the identification of several microbial families characteristic of the compartments upstream of the pelvic flexure that were not represented following it. Our data suggest that the fecal microbiota is not informative of the proximal hindgut but can provide insight into communities of the distal compartments. Further, our results suggest that the pelvic flexure might be an important anatomical landmark relative to the microbial communities in the equine large intestine.}, }
@article {pmid33504454, year = {2021}, author = {Eetemadi, A and Tagkopoulos, I}, title = {Methane and fatty acid metabolism pathways are predictive of Low-FODMAP diet efficacy for patients with irritable bowel syndrome.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {40}, number = {6}, pages = {4414-4421}, doi = {10.1016/j.clnu.2020.12.041}, pmid = {33504454}, issn = {1532-1983}, mesh = {Bacteria/metabolism ; *Diet, Carbohydrate-Restricted ; Fatty Acids, Volatile/*metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/*diet therapy/metabolism/microbiology ; Metabolic Networks and Pathways ; Metagenome ; Methane/*metabolism ; }, abstract = {OBJECTIVE: Identification of microbiota-based biomarkers as predictors of low-FODMAP diet response and design of a diet recommendation strategy for IBS patients.<br><br>DESIGN: We created a compendium of gut microbiome and disease severity data before and after a low-FODMAP diet treatment from published studies followed by unified data processing, statistical analysis and predictive modeling. We employed data-driven methods that solely rely on the compendium data, as well as hypothesis-driven methods that focus on methane and short chain fatty acid (SCFA) metabolism pathways that were implicated in the disease etiology.<br><br>RESULTS: The patient's response to a low-FODMAP diet was predictable using their pre-diet fecal samples with F1 accuracy scores of 0.750 and 0.875 achieved through data-driven and hypothesis-driven predictors, respectively. The fecal microbiome of patients with high response had higher abundance of methane and SCFA metabolism pathways compared to patients with no response (p-values < 6 × 10-3). The genera Ruminococcus 1, Ruminococcaceae UCG-002 and Anaerostipes can be used as predictive biomarkers of diet response. Furthermore, the low-FODMAP diet followers were identifiable given their microbiome data (F1-score of 0.656).<br><br>CONCLUSION: Our integrated data analysis results argue that there are two types of patients, those with high colonic methane and SCFA production, who will respond well on a low-FODMAP diet, and all others, who would benefit a dietary supplementation containing butyrate and propionate, as well as probiotics with SCFA-producing bacteria, such as lactobacillus. This work demonstrates how data integration can lead to novel discoveries and paves the way towards personalized diet recommendations for IBS.}, }
@article {pmid34901097, year = {2021}, author = {Niitsu, T and Kuge, T and Fukushima, K and Matsumoto, Y and Abe, Y and Okamoto, M and Haduki, K and Saito, H and Nitta, T and Kawano, A and Matsuki, T and Motooka, D and Tsujino, K and Miki, K and Nakamura, S and Kida, H and Kumanogoh, A}, title = {Pleural Effusion Caused by Mycolicibacterium mageritense in an Immunocompetent Host: A Case Report.}, journal = {Frontiers in medicine}, volume = {8}, number = {}, pages = {797171}, doi = {10.3389/fmed.2021.797171}, pmid = {34901097}, issn = {2296-858X}, abstract = {Mycolicibacterium mageritense (M. mageritense) is a rare species among rapidly growing mycobacteria, and M. mageritense pleurisy is very rare. Here, we report for the first time, an immunocompetent patient with pleurisy caused by M. mageritense. The patient had no history of immunodeficiency and no recurrence of lung cancer after surgery. However, 8 months after surgery, he developed a new lung shadow and pleurisy. Although whole-genome analysis of the colony cultured from the patient's pleural fluid revealed M. mageritense, we could not identify it in time, resulting in a poor outcome. M. mageritense pleurisy in this case might have occurred via a bulla rupture of the lung lesion because computed tomography of the patient's chest showed pneumothorax and a lung lesion in contact with thoracic cavity. This case emphasized that nontuberculous mycobacterial pleurisy should be considered in the differential diagnoses of pleural effusion even in immunocompetent patients. Advancement of comprehensive and rapid analyses of genomic data from clinical specimens will lead to better treatment strategies.}, }
@article {pmid34901089, year = {2021}, author = {Zhang, Y and Xu, H and Liu, Y and Kang, J and Chen, H and Wang, Z and Cai, D}, title = {Case Report: Fascioliasis Hepatica Precisely Diagnosed by Metagenomic Next-Generation Sequencing and Treated With Albendazole.}, journal = {Frontiers in medicine}, volume = {8}, number = {}, pages = {773145}, doi = {10.3389/fmed.2021.773145}, pmid = {34901089}, issn = {2296-858X}, abstract = {The clinical manifestations of fascioliasis hepatica in humans are unspecific. Traditional diagnosis relies on evidence of live parasites or eggs in the bile or feces. However, due to similar imaging manifestations, they are often misdiagnosed as malignant tumors. Here, we report a case of a 43-year-old woman with fever and space-occupying liver disease. Liver biopsy, parasite-specific antibody screening, and stool testing did not find any pathogens. Therefore, metagenomic next-generation sequencing (mNGS) and routine microbiological examinations were performed. Finally, Fasciola hepatica was only identified by mNGS. The body temperature of the patient and the eosinophil count remained normal, and the space-occupying liver lesions were significantly absorbed after more than 7 months of treatment with albendazole. The details of this case highlight the timely use of mNGS to identify parasites and judge therapeutic effects after treatment, providing important help for clinical decision-making.}, }
@article {pmid34900990, year = {2021}, author = {Liang, Q and Li, J and Zou, Y and Hu, X and Deng, X and Zou, B and Liu, Y and Wei, L and Liang, L and Wen, X}, title = {Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {731867}, doi = {10.3389/fcell.2021.731867}, pmid = {34900990}, issn = {2296-634X}, abstract = {Background: Dry eye disease (DED) is a multifactorial inflammatory disease of the ocular surface. It is hypothesized that dysbiosis of the conjunctival microbiota contributes to the development of DED. However, species-level compositions of the conjunctival microbiota in DED and the potential dysbiosis involving microorganisms other than bacteria remain largely uncharacterized. Methods: We collected conjunctival impression samples from a cohort of 95 individuals, including 47 patients with DED and 48 healthy subjects. We examined the conjunctival microbiota of these samples using shotgun metagenomic sequencing and analyzed microbial dysbiosis in DED at the species level. Results: The conjunctival microbiota in DED exhibited a decreased α-diversity and an increased inter-individual variation. The α-diversity of female patients with DED was higher than that of male patients. Despite a decreased prevalence in DED, 23 microbial species were identified to show abnormally high abundance in DED samples positive for the species. Among these species, a fungal species Malassezia globosa was enriched female patients. In addition, distinct patterns of associations with disease status were observed for different species of the same genus. For DED subtypes, Staphylococcus aureus and S. capitis were associated with meibomian gland dysfunction (MGD), whereas S. hominis was enriched in patients solely with aqueous tear deficiency (ATD). The microbiota of patients with a mixed type of diagnosis was more similar to MGD patients than ATD patients. Conclusion: We demonstrated that the conjunctival microbiota dysbiosis in DED is characterized by significant heterogeneity. Microbial signatures may offer novel insights into the complicated etiology of DED and potentially promote the development of personalized treatment for DED in the future.}, }
@article {pmid34900412, year = {2021}, author = {Yildirim, E and Ilina, L and Laptev, G and Filippova, V and Brazhnik, E and Dunyashev, T and Dubrovin, A and Novikova, N and Tiurina, D and Tarlavin, N and Laishev, K}, title = {The structure and functional profile of ruminal microbiota in young and adult reindeers (Rangifer tarandus) consuming natural winter-spring and summer-autumn seasonal diets.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12389}, doi = {10.7717/peerj.12389}, pmid = {34900412}, issn = {2167-8359}, abstract = {Background: The key natural area of Russian reindeer (Rangifer tarandus, Nenets breed) is arctic zones, with severe climatic conditions and scarce feed resources, especially in the cold winter season. The adaptation of reindeer to these conditions is associated not only with the genetic potential of the animal itself. The rumen microbiome provides significant assistance in adapting animals to difficult conditions by participating in the fiber digestion. The aim of our study is to investigate the taxonomy and predicted metabolic pathways of the ruminal microbiota (RM) during the winter-spring (WS) and summer-autumn (SA) seasons, in calves and adult reindeer inhabiting the natural pastures of the Yamalo-Nenetsky Autonomous District of the Russian Federation.<br><br>Methods: The RM in reindeer was studied using the Next Generation Sequencing method with the MiSeq (Illumina, San Diego, CA, USA) platform. Reconstruction and prediction of functional profiles of the metagenome, gene families, and enzymes were performed using the software package PICRUSt2 (v.2.3.0).<br><br>Results: The nutritional value of WS and SA diets significantly differed. Crude fiber content in the WS diet was higher by 22.4% (p < 0.05), compared to SA, indicating possibly poorer digestibility and necessity of the adaptation of the RM to this seasonal change. A total of 22 bacterial superphyla and phyla were found in the rumen, superphylum Bacteroidota and phylum Firmicutes being the dominating taxa (up to 48.1% ± 4.30% and 46.1% ± 4.80%, respectively); while only two archaeal phyla presented as minor communities (no more then 0.54% ± 0.14% totally). The percentages of the dominating taxa were not affected by age or season. However, significant changes in certain minor communities were found, with seasonal changes being more significant than age-related ones. The percentage of phylum Actinobacteriota significantly increased (19.3-fold) in SA, compared to WS (p = 0.02) in adults, and the percentage of phylum Cyanobacteria increased up to seven-fold (p = 0.002) in adults and calves. Seasonal changes in RM can improve the ability of reindeer to withstand the seasons characterized by a low availability of nutrients. The PICRUSt2 results revealed 257 predicted metabolic pathways in RM: 41 pathways were significantly (p < 0.05) influenced by season and/or age, including the processes of synthesis of vitamins, volatile fatty acids, and pigments; metabolism of protein, lipids, and energy; pathogenesis, methanogenesis, butanediol to pyruvate biosynthesis, cell wall biosynthesis, degradation of neurotransmitters, lactic acid fermentation, and biosynthesis of nucleic acids. A large part of these changeable pathways (13 of 41) was related to the synthesis of vitamin K homologues.<br><br>Conclusion: The results obtained improve our knowledge on the structure and possible metabolic pathways of the RM in reindeer, in relation to seasonal changes.}, }
@article {pmid34900140, year = {2021}, author = {Yang, C and Chowdhury, D and Zhang, Z and Cheung, WK and Lu, A and Bian, Z and Zhang, L}, title = {A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {6301-6314}, doi = {10.1016/j.csbj.2021.11.028}, pmid = {34900140}, issn = {2001-0370}, abstract = {Metagenomic sequencing provides a culture-independent avenue to investigate the complex microbial communities by constructing metagenome-assembled genomes (MAGs). A MAG represents a microbial genome by a group of sequences from genome assembly with similar characteristics. It enables us to identify novel species and understand their potential functions in a dynamic ecosystem. Many computational tools have been developed to construct and annotate MAGs from metagenomic sequencing, however, there is a prominent gap to comprehensively introduce their background and practical performance. In this paper, we have thoroughly investigated the computational tools designed for both upstream and downstream analyses, including metagenome assembly, metagenome binning, gene prediction, functional annotation, taxonomic classification, and profiling. We have categorized the commonly used tools into unique groups based on their functional background and introduced the underlying core algorithms and associated information to demonstrate a comparative outlook. Furthermore, we have emphasized the computational requisition and offered guidance to the users to select the most efficient tools. Finally, we have indicated current limitations, potential solutions, and future perspectives for further improving the tools of MAG construction and annotation. We believe that our work provides a consolidated resource for the current stage of MAG studies and shed light on the future development of more effective MAG analysis tools on metagenomic sequencing.}, }
@article {pmid34899675, year = {2021}, author = {Pasquali, F and Remondini, D and Snary, EL and Hald, T and Guillier, L}, title = {Editorial: Integrating Whole Genome Sequencing Into Source Attribution and Risk Assessment of Foodborne Bacterial Pathogens.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {795098}, doi = {10.3389/fmicb.2021.795098}, pmid = {34899675}, issn = {1664-302X}, }
@article {pmid34899652, year = {2021}, author = {DeCastro, ME and Escuder-Rodríguez, JJ and Becerra, M and Rodríguez-Belmonte, E and González-Siso, MI}, title = {Comparative Metagenomic Analysis of Two Hot Springs From Ourense (Northwestern Spain) and Others Worldwide.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {769065}, doi = {10.3389/fmicb.2021.769065}, pmid = {34899652}, issn = {1664-302X}, abstract = {With their circumneutral pH and their moderate temperature (66 and 68°C, respectively), As Burgas and Muiño da Veiga are two important human-use hot springs, previously studied with traditional culture methods, but never explored with a metagenomic approach. In the present study, we have performed metagenomic sequence-based analyses to compare the taxonomic composition and functional potential of these hot springs. Proteobacteria, Deinococcus-Thermus, Firmicutes, Nitrospirae, and Aquificae are the dominant phyla in both geothermal springs, but there is a significant difference in the abundance of these phyla between As Burgas and Muiño da Veiga. Phylum Proteobacteria dominates As Burgas ecosystem while Aquificae is the most abundant phylum in Muiño da Veiga. Taxonomic and functional analyses reveal that the variability in water geochemistry might be shaping the differences in the microbial communities inhabiting these geothermal springs. The content in organic compounds of As Burgas water promotes the presence of heterotrophic populations of the genera Acidovorax and Thermus, whereas the sulfate-rich water of Muiño da Veiga favors the co-dominance of genera Sulfurihydrogenibium and Thermodesulfovibrio. Differences in ammonia concentration exert a selective pressure toward the growth of nitrogen-fixing bacteria such as Thermodesulfovibrio in Muiño da Veiga. Temperature and pH are two important factors shaping hot springs microbial communities as was determined by comparative analysis with other thermal springs.}, }
@article {pmid34899641, year = {2021}, author = {Xie, BB and Li, M and Anantharaman, K and Ravin, NV}, title = {Editorial: The Uncultured Microorganisms: Novel Technologies and Applications.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {756287}, doi = {10.3389/fmicb.2021.756287}, pmid = {34899641}, issn = {1664-302X}, }
@article {pmid34897962, year = {2021}, author = {Sahu, RP and Kazy, SK and Bose, H and Mandal, S and Dutta, A and Saha, A and Roy, S and Gupta, SD and Mukherjee, A and Sar, P}, title = {Microbial diversity and function in crystalline basement beneath the Deccan Traps explored in a 3-km borehole at Koyna, western India.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15867}, pmid = {34897962}, issn = {1462-2920}, abstract = {Deep terrestrial subsurface represents a huge repository of global prokaryotic biomass. Given its vastness and importance, microbial life within the deep-subsurface continental crust remains under represented in global studies. We characterize the microbial communities of deep, extreme and oligotrophic realm hosted by crystalline Archaean granitic rocks underneath the Deccan Traps, through sampling via 3000 meter deep scientific borehole at Koyna, India through metagenomics, amplicon sequencing, and cultivation-based analyses. 16S rRNA gene sequences (7.37 × 106) show considerable bacterial diversity and existence of a core microbiome (5724 operational taxonomic units conserved out of a total 118064 OTUs) across the depths. Relative abundance of different taxa of core microbiome varies with depth in response to prevailing lithology and geochemistry. Co-occurrence network analysis and cultivation attempt elucidate close interactions among autotrophic and organotrophic bacteria. Shotgun metagenomics reveals major role of autotrophic carbon fixation via the Wood-Ljungdahl pathway and genes responsible for energy and carbon metabolism. Deeper analysis suggests the existence of an 'acetate switch', coordinating biosynthesis and cellular homeostasis. We conclude that the microbial life in the nutrient- and energy-limited deep granitic crust is constrained by the depth and managed by a few core members via a close interplay between autotrophy and organotrophy. This article is protected by copyright. All rights reserved.}, }
@article {pmid34897914, year = {2021}, author = {Li, R and Zheng, M and Zheng, M and Cai, R and Cui, X and Wang, Y and Jiang, X and Xu, C}, title = {Metagenomic analysis reveals the linkages between bacteria and the functional enzymes responsible for potential ammonia and biogenic amine production in alfalfa silage.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.15411}, pmid = {34897914}, issn = {1365-2672}, abstract = {AIMS: To clarify the molecular mechanisms underlying ammonia (NH3) and biogenic amines (BAEs) formation in alfalfa silage, whole metagenomic sequencing analysis was performed to identify the linkages between functional bacteria and their responsible enzymes in alfalfa silage prepared with and without sucrose addition.<br><br>METHODS AND RESULTS: Genes encoding nitrite reductase (nirB) resulting in NH3 formation were the most abundant and were mostly assigned to Enterobacter cloacae and Klebsiella oxytoca. Putrescine-related genes, classified mainly to encode ornithine decarboxylase (odcA), were predominantly carried by Escherichia coli, Ent. cloacae, and Citrobacter sp.. E. coli and Kl. oxytoca were the important species responsible for cadaverine and tyramine formation. Ent. cloacae, E. coli, and Kl. oxytoca dominated the bacterial community in naturally fermented alfalfa silage, while sucrose-treated silages greatly inhibited the growth of these species by promoting the dominance of Lactobacillus plantarum, thus decreasing the concentrations of NH3 , cadaverine, putrescine, and tyramine.<br><br>CONCLUSIONS: Enterobacteriaceae bacteria are mainly responsible for the NH3 , putrescine, cadaverine and tyramine formations in alfalfa silage.<br><br>Whole metagenomic sequencing analysis served as a useful tool to identify the linkages between functional bacteria and associated enzymes responsible for NH3 and BAEs formation.}, }
@article {pmid34897253, year = {2021}, author = {Moradi, Z and Mehrvar, M}, title = {Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of Vinca minor and Wisteria sinensis in Iran: with Implications for the Genetic Structure of the Virus.}, journal = {The plant pathology journal}, volume = {37}, number = {6}, pages = {619-631}, doi = {10.5423/PPJ.OA.10.2021.0151}, pmid = {34897253}, issn = {1598-2254}, support = {01-1400-03//Sari Agricultural Sciences and Natural Resources University/ ; }, abstract = {Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23-99.26% and 98.04-98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96-98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.}, }
@article {pmid34896845, year = {2021}, author = {Lai, J and Li, A and Jiang, J and Yuan, X and Zhang, P and Xi, C and Wu, L and Wang, Z and Chen, J and Lu, J and Lu, S and Mou, T and Zhou, H and Wang, D and Huang, M and Dong, F and Li, MD and Xu, Y and Song, X and Hu, S}, title = {Metagenomic analysis reveals gut bacterial signatures for diagnosis and treatment outcome prediction in bipolar depression.}, journal = {Psychiatry research}, volume = {307}, number = {}, pages = {114326}, doi = {10.1016/j.psychres.2021.114326}, pmid = {34896845}, issn = {1872-7123}, abstract = {BACKGROUND: We aimed to characterize gut microbial alterations in depressed patients with bipolar disorder (BD) following quetiapine monotherapy and explored its potential for disease diagnosis and outcome prediction.<br><br>METHODS: Fecal samples were obtained from 60 healthy individuals and 62 patients in acute depressive episodes. All patients received one-month quetiapine treatment after enrollment. The structure of gut microbiota was measured with metagenomic sequencing, and its correlation with clinical profiles and brain function as indicated by resting-state functional magnetic resonance imaging was analyzed. Random forest models based on bacterial species were constructed to distinguish patients from controls, and responders from non-responders, respectively.<br><br>RESULTS: BD patients displayed specific alterations in gut microbial diversity and composition. Quetiapine treatment increased the diversity of microbial communities and changed the composition. The abundance of Clostridium bartlettii was negatively associated with age, baseline depression severity, while positively associated with spontaneous neural oscillation in the hippocampus. Tree-based classification models for (1) patients and controls and (2) responders and non-responders showed an area under the curve of 0.733 and 0.800, respectively.<br><br>CONCLUSION: Our findings add new evidence to the existing literature regarding gut dysbiosis in BD and reveal the potential of microbe-based biomarkers for disease diagnosis and treatment outcome prediction.}, }
@article {pmid34896510, year = {2021}, author = {Zhou, L and Xu, P and Gong, J and Huang, S and Chen, W and Fu, B and Zhao, Z and Huang, X}, title = {Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152263}, doi = {10.1016/j.scitotenv.2021.152263}, pmid = {34896510}, issn = {1879-1026}, abstract = {Estuaries are resistome hotspots owing to resistome accumulation and propagation at these locations from surrounding rivers, yet the large-scale biogeographic pattern of resistome, especially biocide and metal resistance genes (BMRGs) and its driving mechanisms in estuarine waters remains to be elucidated. Here, a metagenomics-based approach was firstly used to investigate resistome and mobilome profiles in waters from 30 subtropical estuaries, South China. The Pearl River estuaries had a higher diversity and abundance of antibiotic resistance genes (ARGs), BMRGs, and mobile genetic elements (MGEs) when compared with estuaries from east and west regions. Genes resistant to multiple antibiotics, metals, and biocides were the most abundant gene types in the resistome. The abundance of MGEs (e.g., intI1, IS91, and tnpA) was highly associated with the total abundance of resistance genes, suggesting their utility as potential indicators for quantitative estimations of the resistome contamination. Further, MGEs contributed more than bacterial communities in shaping the resistome in subtropical estuaries. Physicochemical factors (e.g., pH) regulated MGE composition and stochastic assembly, which mediated the co-selection of ARGs and BMRGs via horizontal gene transfer. Our findings have important implications and provide a reference on the management of ARGs and BMRGs in subtropical estuarine ecosystems.}, }
@article {pmid34896501, year = {2021}, author = {Bagi, A and Knapik, K and Baussant, T}, title = {Abundance and diversity of n-alkane and PAH-degrading bacteria and their functional genes - Potential for use in detection of marine oil pollution.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152238}, doi = {10.1016/j.scitotenv.2021.152238}, pmid = {34896501}, issn = {1879-1026}, abstract = {Monitoring environmental status through molecular investigation of microorganisms in the marine environment is suggested as a potentially very effective method for biomonitoring, with great potential for automation. There are several hurdles to that approach with regards to primer design, variability across geographical locations, seasons, and type of environmental pollution. Here, qPCR analysis of genes involved in the initial activation of aliphatic and aromatic hydrocarbons were used in a laboratory setup mimicking realistic oil leakage at sea. Seawater incubation experiments were carried out under two different seasons with two different oil types. Degenerate primers targeting initial oxygenases (alkane 1-monooxygenase; alkB and aromatic-ring hydroxylating dioxygenase; ARHD) were employed in qPCR assays to quantify the abundance of genes essential for oil degradation. Shotgun metagenomics was used to map the overall community dynamics and the diversity of alkB and ARHD genes represented in the microbial community. The amplicons generated through the qPCR assays were sequenced to reveal the diversity of oil-degradation related genes captured by the degenerate primers. We identified a major mismatch between the taxonomic diversity of alkB and ARHD genes amplified by the degenerate primers and those identified through shotgun metagenomics. More specifically, the designed primers did not amplify the alkB genes of the two most abundant alkane degraders that bloomed in the experiments, Oceanobacter and Oleispira. The relative abundance of alkB sequences from shotgun metagenomics and 16S rRNA-based Oleispira-specific qPCR assay were better signals for oil in water than the tested qPCR alkB assay. The ARHD assay showed a good agreement with PAHs degradation despite covering only 25% of the top 100 ARHD genes and missing several abundant Cycloclasticus sequences that were present in the metagenome. We conclude that further improvement of the degenerate primer approach is needed to rely on the use of oxygenase-related qPCR assays for oil leakage detection.}, }
@article {pmid34896404, year = {2021}, author = {Demir, M and Lang, S and Hartmann, P and Duan, Y and Martin, A and Miyamoto, Y and Bondareva, M and Zhang, X and Wang, Y and Kasper, P and Bang, C and Roderburg, C and Tacke, F and Steffen, HM and Goeser, T and Kruglov, A and Eckmann, L and Stärkel, P and Fouts, DE and Schnabl, B}, title = {The fecal mycobiome in non-alcoholic fatty liver disease.}, journal = {Journal of hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhep.2021.11.029}, pmid = {34896404}, issn = {1600-0641}, abstract = {BACKGROUND &amp; AIMS: Studies investigating the gut-liver axis have largely focused on bacteria, whereas little is known about commensal fungi. We characterized fecal fungi in patients with non-alcoholic fatty liver disease (NAFLD) and investigated their role in a fecal microbiome-humanized mouse model of Western diet-induced steatohepatitis.<br><br>METHODS: We performed fungal internal transcribed spacer 2 sequencing using fecal samples from 78 NAFLD patients, 16 controls and 73 patients with alcohol use disorder (AUD). Anti-Candida albicans (C. albicans) IgG was measured in blood samples from 17 controls and 79 NAFLD patients. Songbird, a novel multinominal regression tool, was used to investigate mycobiome changes. Germ-free mice were colonized with feces from patients with non-alcoholic steatohepatitis (NASH), fed a Western diet for 20 weeks and treated with the anti-fungal amphotericin B.<br><br>RESULTS: The presence of non-obese NASH or F2-F4 fibrosis was associated with a distinct fecal mycobiome signature. Changes were characterized by an increased log-ratio for Mucor sp./Saccharomyces cerevisiae (S. cerevisiae) in patients with NASH and F2-F4 fibrosis. The C. albicans/S. cerevisiae log-ratio was significantly higher in non-obese patients with NASH when compared with non-obese patients with NAFL or controls. We observed a different fecal mycobiome composition in NAFLD patients with advanced fibrosis as compared with AUD patients and advanced fibrosis. Plasma anti-C. albicans IgG was increased in NAFLD patients with advanced fibrosis. Gnotobiotic mice, colonized with human NASH feces and treated with amphotericin B were protected from Western diet-induced steatohepatitis.<br><br>CONCLUSIONS: Non-obese NAFLD patients with more advanced disease have a different fecal mycobiome composition than non-obese NAFLD patients with mild disease. Antifungal treatment ameliorates diet-induced steatohepatitis in mice. Intestinal fungi could be an attractive target to attenuate NASH.<br><br>LAY SUMMARY: Non-alcoholic fatty liver disease is one of the most common chronic liver diseases and is associated with changes in the fecal bacterial microbiome. We show that patients with non-alcoholic fatty liver disease and more severe disease stages have a specific composition of fecal fungi and an increased systemic immune response to Candida albicans. In a fecal microbiome-humanized mouse model of Western-diet induced steatohepatitis, we show that treatment with antifungals reduces liver damage.}, }
@article {pmid34896259, year = {2021}, author = {Yu, J and Liu, J and Senthil Kumar, P and Wei, Y and Zhou, M and Vo, DN and Xiao, L}, title = {Promotion of methane production by magnetite via increasing acetogenesis revealed by metagenome-assembled genomes.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {126521}, doi = {10.1016/j.biortech.2021.126521}, pmid = {34896259}, issn = {1873-2976}, abstract = {Metal oxides are wildly studied to enhance anaerobic digestion and the methanogenic process, which is generally interpreted by increased direct interspecies electron transfer (DIET). Yet microbial mechanisms involved are under debate. Herein, ethane production dynamics were analyzed, and acceleration on biogas accumulation was presented. Complementing previous findings, Fe3O4 nanoparticles stimulated bacterial fermentation rather than methanogenesis or syntropy between electro-microorganism and methanogen. More importantly, metagenome-assembled genomes proved that Fe3O4 nanoparticles increased acetogenesis by Parabacteroides chartae, which provided abundant substrates for acetoclastic methanogenesis. Interestingly, the weakly conductive V3O7·H2O nanowires increased potential hydrogen-producing bacteria, Brevundimonas, and electro-microorganisms, Clostridium and Rhodoferax, which is convenient for conducting DIET. Collectively, conductivity may not be a critical factor in mediating DIET and distinct strategies of metal oxides on methane production propose more possibilities, such as fermentation process, waste treatment, and renewable energy recovery.}, }
@article {pmid34896003, year = {2021}, author = {Kirby, TO and Shi, X and Walters, D and Roullet, JB and Gibson, KM}, title = {Intestinal Dysbiosis as a component of pathophysiology in succinic semialdehyde dehydrogenase deficiency (SSADHD).}, journal = {Molecular genetics and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ymgme.2021.11.355}, pmid = {34896003}, issn = {1096-7206}, abstract = {Succinic semialdehyde dehydrogenase deficiency (SSADHD) is an inherited inborn error of the γ-aminobutyric acid (GABA) metabolism pathway. It results from mutations in the ALDH5A1 gene leading to elevated GABA, γ-hydroxybutyric acid (GHB), succinic semialdehyde (SSA), decreased glutamine and alterations in several other metabolites. The phenotype includes developmental and cognitive delays, hypotonia, seizures, neuropsychiatric morbidity and other nervous system pathologies. The composition of the intestinal flora of patients with SSADHD has not been characterized, and dysbiosis of the gut microbiome may unveil novel treatment paradigms. We investigated the gut microbiome in SSADHD using 16S ribosomal DNA sequencing and unmasked evidence of dysbiosis in both aldh5a1-deficient mice and patients with SSADHD. In the murine model, there was a reduction in α-diversity measurements, and there were 4 phyla, 3 classes, 5 orders, 9 families, and 15 genera that differed, with a total of 17 predicted metabolic pathways altered. In patients, there were changes in Fusobacterium, 3 classes, 4 orders, 11 families, and a predicted alteration in genes associated with the digestive system. We believe this is the first evaluation of microbiome structure in an IEM with a neurometabolic phenotype that is not treated dietarily.}, }
@article {pmid34894514, year = {2021}, author = {Zhu, W and Yang, D and Chang, L and Zhang, M and Zhu, L and Jiang, J}, title = {Animal gut microbiome mediates the effects of antibiotic pollution on an artificial freshwater system.}, journal = {Journal of hazardous materials}, volume = {425}, number = {}, pages = {127968}, doi = {10.1016/j.jhazmat.2021.127968}, pmid = {34894514}, issn = {1873-3336}, abstract = {The antibiotic pollution has become an emerging environmental problem worldwide, but the ecological outcomes remain to be elucidated, especially very little is known about the interactions between antibiotics and different ecological elements. In this study, the long-term influences of three representative antibiotics, i.e., tetracycline, erythromycin, and sulfamethoxazole, were investigated focusing on a simplified artificial freshwater system composed of amphibian tadpoles, gut and environmental bacterial and fungi communities, and water parameters. Results demonstrated that antibiotic exposure reduced tadpole's fitness with increased mortality and physiological abnormality, and altered the water quality, particularly the nitrogen homeostasis. Sequential analyses at organism, symbiont, and systematic levels revealed that antibiotics disrupted tadpole metabolome (e.g., tetrahydrobiopterin metabolism) directly by off-target effects. Antibiotics also reshaped the tadpole gut bacterial and fungi diversity and composition, which partly accounted for the tadpole's health condition. Moreover, changes of tadpole gut microbiome (i.e., Cyanobacteria and Basidiomycota OTUs) partly explained the variations of water parameters. In contrast, environmental microbiota and metagenome stayed relatively stable, and didn't contribute to the environmental variations. These results highlighted the pivotal role of gut microbiome in mediating the effects of antibiotics on the host and the environment, which would extend our understanding on the ecological outcomes caused by antibiotic pollution.}, }
@article {pmid34893089, year = {2021}, author = {Wang, Z and Usyk, M and Vázquez-Baeza, Y and Chen, GC and Isasi, CR and Williams-Nguyen, JS and Hua, S and McDonald, D and Thyagarajan, B and Daviglus, ML and Cai, J and North, KE and Wang, T and Knight, R and Burk, RD and Kaplan, RC and Qi, Q}, title = {Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {336}, pmid = {34893089}, issn = {1474-760X}, support = {HHSN268201300002I/N01-HC-65235/HL/NHLBI NIH HHS/United States ; R01-HL140976/HL/NHLBI NIH HHS/United States ; R01-HL060712//National Heart, Lung, and Blood Institute (US)/ ; }, abstract = {BACKGROUND: Obesity and related comorbidities are major health concerns among many US immigrant populations. Emerging evidence suggests a potential involvement of the gut microbiome. Here, we evaluated gut microbiome features and their associations with immigration, dietary intake, and obesity in 2640 individuals from a population-based study of US Hispanics/Latinos.<br><br>RESULTS: The fecal shotgun metagenomics data indicate that greater US exposure is associated with reduced ɑ-diversity, reduced functions of fiber degradation, and alterations in individual taxa, potentially related to a westernized diet. However, a majority of gut bacterial genera show paradoxical associations, being reduced with US exposure and increased with fiber intake, but increased with obesity. The observed paradoxical associations are not explained by host characteristics or variation in bacterial species but might be related to potential microbial co-occurrence, as seen by positive correlations among Roseburia, Prevotella, Dorea, and Coprococcus. In the conditional analysis with mutual adjustment, including all genera associated with both obesity and US exposure in the same model, the positive associations of Roseburia and Prevotella with obesity did not persist, suggesting that their positive associations with obesity might be due to their co-occurrence and correlations with obesity-related taxa, such as Dorea and Coprococcus.<br><br>CONCLUSIONS: Among US Hispanics/Latinos, US exposure is associated with unfavorable gut microbiome profiles for obesity risk, potentially related to westernized diet during acculturation. Microbial co-occurrence could be an important factor to consider in future studies relating individual gut microbiome taxa to environmental factors and host health and disease.}, }
@article {pmid34893078, year = {2021}, author = {Wu, N and Ranjan, P and Tao, C and Liu, C and Yang, E and He, B and Erb-Downward, JR and Bo, S and Zheng, J and Guo, C and Liu, B and Sun, L and Yan, W and Wang, M and Wang, W and Wen, J and Yang, P and Yang, L and Tian, Q and Dickson, RP and Shen, N}, title = {Rapid identification of pathogens associated with ventilator-associated pneumonia by Nanopore sequencing.}, journal = {Respiratory research}, volume = {22}, number = {1}, pages = {310}, pmid = {34893078}, issn = {1465-993X}, abstract = {BACKGROUND: Aetiology detection is crucial in the diagnosis and treatment of ventilator-associated pneumonia (VAP). However, the detection method needs improvement. In this study, we used Nanopore sequencing to build a quick detection protocol and compared the efficiency of different methods for detecting 7 VAP pathogens.<br><br>METHODS: The endotracheal aspirate (ETA) of 83 patients with suspected VAP from Peking University Third Hospital (PUTH) was collected, saponins were used to deplete host genomes, and PCR- or non-PCR-amplified library construction methods were used and compared. Sequence was performed with MinION equipment and local data analysis methods were used for sequencing and data analysis.<br><br>RESULTS: Saponin depletion effectively removed 11 of 12 human genomes, while most pathogenic bacterial genome results showed no significant difference except for S. pneumoniae. Moreover, the average sequence time decreased from 19.6 h to 3.62 h. The non-PCR amplification method and PCR amplification method for library build has a similar average sensitivity (85.8% vs. 86.35%), but the non-PCR amplification method has a better average specificity (100% VS 91.15%), and required less time. The whole method takes 5-6 h from ETA extraction to pathogen classification. After analysing the 7 pathogens enrolled in our study, the average sensitivity of metagenomic sequencing was approximately 2.4 times higher than that of clinical culture (89.15% vs. 37.77%), and the average specificity was 98.8%.<br><br>CONCLUSIONS: Using saponins to remove the human genome and a non-PCR amplification method to build libraries can be used for the identification of pathogens in the ETA of VAP patients within 6 h by MinION, which provides a new approach for the rapid identification of pathogens in clinical departments.}, }
@article {pmid34890655, year = {2021}, author = {Yang, Y and Che, Y and Liu, L and Wang, C and Yin, X and Deng, Y and Yang, C and Zhang, T}, title = {Rapid absolute quantification of pathogens and ARGs by nanopore sequencing.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152190}, doi = {10.1016/j.scitotenv.2021.152190}, pmid = {34890655}, issn = {1879-1026}, abstract = {Compositional nature of relative abundance data in the current standard microbiome studies limits microbial dynamics interpretations and cross-sample comparisons. Here, we demonstrate the first rapid (1-h sequencing) method coupling Nanopore metagenomic sequencing with cellular spike-in to facilitate the absolute quantification and removal assessment of pathogens and antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). Nanopore sequencing-based quantification results for both simple mock community and complex real environmental samples showed a high consistency with those from the widely-used Illumina and culture-based approaches. Implementing such method, we quantified 46 predominant putative pathogenic species, and 361 ARGs in three WWTP sample sets. Though high log removals of dominant pathogens (2.23 logs) and ARGs (1.98 logs) were achieved, complete removal of all pathogens and ARGs were not achieved. Noticeably, Mycobacterium spp., Clostridium_P perfringens, and Borrelia hermsii exhibited low removal, and 13 ARGs even increased in absolute abundance after the treatment. Our proposed approach manifested its profound ability in providing absolute quantitation information guiding wastewater-based epidemiological surveillance and quantitative risk assessment facilitating microbial hazards management.}, }
@article {pmid34890652, year = {2021}, author = {Zhang, M and Guo, H and Xia, D and Dong, Z and Liu, X and Zhao, W and Jia, J and Yin, X}, title = {Metagenomic insight of corn straw conditioning on substrates metabolism during coal anaerobic fermentation.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152220}, doi = {10.1016/j.scitotenv.2021.152220}, pmid = {34890652}, issn = {1879-1026}, abstract = {Increasing methane production from anaerobic digestion of coal is challenging. This study shows that the combined fermentation of coal and corn straw greatly enriched the substrates available to microorganisms. This was mainly manifested in the increased types and abundance of organic matter in the fermentation liquid, which enhanced methane production by 61%. Metagenomic analysis showed that the addition of corn straw enriched the abundance of Methanosarcina in the combined fermentation system and promoted the complementary advantages of the microorganisms. At the same time, the abundance of genes that convert glucose into acetic acid (K00927, K01689, K01905, etc.) in the combined fermentation system increased, which is conducive to acidification process and biomethane production. In addition, there were the two key methanogenic pathways, namely aceticlastic (57.1%-63.5%) and hydrogenotrophic (23.4%-25.1%) methanogenesis, identified in the single coal fermentation system and the combined coal and corn straw fermentation system. Combined fermentation enhanced the hydrogenotrophic and methylotrophic methanogenic pathways by increasing the gene abundance of K00200 (methane production from CO2 and oxidation of coenzyme M to CO2), K00440 (participates in the binding to other known physiological receptors with hydrogen as a donor), and K00577 (methyltransferase).}, }
@article {pmid34890650, year = {2021}, author = {Xu, S and Liu, Y and Wang, R and Zhang, T and Lu, W}, title = {Behaviors of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) during the pilot-scale biophysical drying treatment of sewage sludge: Reduction of ARGs and enrichment of MRGs.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {152221}, doi = {10.1016/j.scitotenv.2021.152221}, pmid = {34890650}, issn = {1879-1026}, abstract = {Biophysical drying (BPD) is one of the best alternatives for reducing the moisture content from sewage sludge by utilizing biological heat from aerobic reactions. However, the fate of emerging pollutants during BPD process is largely unknown. In this study, the fates of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were investigated during a pilot-scale BPD treatment of sewage sludge. A total of 20 types (388 subtypes) of ARGs and 16 types (364 subtypes) of MRGs were detected by metagenomic sequencing and annotation. The total abundance of ARGs decreased from 1.78 ± 0.13 copies/16S rRNA to 0.55 ± 0.01 copies/16S rRNA and meanwhile, the total abundance of MRGs increased from 3.81 ± 0.01 copies/16S rRNA to 6.30 ± 0.02 copies/16S rRNA, showing the distinct behaviors of ARGs and MRGs during BPD process. The ARGs were effectively reduced during the mesophilic and thermophilic stages of BPD process and the reduction of ARGs fitted the first-order kinetic model (p < 0.01). Microbial community analysis showed that the abundance of potential pathogens was also decreased during BPD process. On the contrary, the abundances of most MRG subtypes (78.3%) were enriched during BPD process with up to 122-fold change, implying the potential threats for the end product of BPD process. These results together indicate that although the ARGs and potential pathogens can be effectively reduced during BPD process, the safety for the end product still needs to be considered due to the enrichment of MRGs.}, }
@article {pmid34890626, year = {2021}, author = {Howard, B and Bascom, CC and Hu, P and Binder, RL and Fadayel, G and Huggins, TG and Jarrold, BB and Osborne, R and Rocchetta, HL and Swift, D and Tiesman, JP and Song, Y and Wang, Y and Wehmeyer, K and Kimball, AB and Isfort, RJ}, title = {Aging Associated Changes in the Adult Human Skin Microbiome and the Host Factors That Affect Skin Microbiome Composition.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2021.11.029}, pmid = {34890626}, issn = {1523-1747}, abstract = {Understanding changes in the skin microbiome and their relationship to host skin factors during aging remains largely unknown. To better understand this phenomenon, we collected samples for metagenomic and host skin factor analyses from forearm, buttock, and facial skin from 158 Caucasian females at 20-24, 30-34, 40-44, 50-54, 60-64, and 70-74 years of age. Metagenomics analysis was performed using 16S rRNA gene sequencing, while host sebocyte gland area, skin lipids, natural moisturizing factors (NMFs) and anti-microbial peptides (AMPs) measurements were also performed. These analyses demonstrated that skin bacterial diversity increased at all the skin sites with increasing age. Of the bacterial genera with average relative abundance of >1%, only Lactobacillus and Cutibacterium demonstrated a significant change (decrease) in abundance at all sampled skin sites with increasing age. Additional bacterial genera demonstrated significant age and site-specific changes in abundance. Analysis of sebocyte area, NMFs, lipids and AMPs demonstrated an age-related decrease in sebocyte area and increases in NMFs/AMPs/skin lipids, all which correlated with changes in specific bacterial genera. In conclusion, the human skin microbiome undergoes age-associated alterations that may reflect underlying age-related changes in cutaneous biology.}, }
@article {pmid34890617, year = {2021}, author = {Muthukumar, B and Parthipan, P and AlSalhi, MS and Prabhu, NS and Rao, TN and Devanesan, S and Maruthamuthu, MK and Rajasekar, A}, title = {Characterization of bacterial community in oil-contaminated soil and its biodegradation efficiency of high molecular weight (&gt;C40) hydrocarbon.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {133168}, doi = {10.1016/j.chemosphere.2021.133168}, pmid = {34890617}, issn = {1879-1298}, abstract = {In this study, two biosurfactant producing Pseudomonas aeruginosa sp. were isolated from motor oil contaminated soil for crude oil, alkane and PAH degradation studies. Metagenomics analysis identified as phyla proteobacteria was the dominant. Isolated two bacterial species were well grown in mineral salt medium with 1% of crude oil, alkanes (dotriacontane and tetratetracontane) and PAH (pyrene, benzopyrene and anthracene) as sole carbon sources. Total biodegradation efficiency (BE) of strains pp3 and pp4 in Crude oil degradation evaluated by the analysis of gas chromatography and mass spectrometry was 50% and 86% respectively. BE of pp3, pp4 and mixed consortium in alkane biodegradation were 46%, 47% and 36% respectively. BE of pp3, pp4 and mixed consortium in PAH biodegradation were 22%, 48% and 35% respectively. Based on the results revealed that strain pp4 was more efficient bacteria to degrade the crude oil, alkane and PAH than pp3. This was due to the higher production of biosurfactant by pp4 than pp3 and also confirmed in the test of emulsification index (E24). FTIR results showed that the produced biosurfactant could partially solubilize the crude oil hydrocarbons, alkanes and PAH and confirmed as biosurfactant are glycolipid (rhamnolipid). Thus, the obtained results from the GCMS showed that all hydrocarbons were utilized by bacteria as carbon source for biosurfactant production and utilize the high molecular weight hydrocarbons. Based on the present study we can suggest that identified potential biosurfactant producing bacteria are used for biodegradation of high molecular weight hydrocarbon (>C40).}, }
@article {pmid34890483, year = {2021}, author = {Shen, Z and Wang, F and Liang, Y and Li, Y and Liu, Q and Liu, F}, title = {Diversity and functions of microbes in surface sediments under heavy metal pollution of western Chaohu Lake.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/lam.13627}, pmid = {34890483}, issn = {1472-765X}, abstract = {Heavy metal pollution is a global concern. Targeting at the surface sediments in western Chaohu Lake and using metagenome sequencing, we probed into the mechanism how microbes adapted to heavy-metal-polluted sediments under natural conditions. It was found the heavy metal pollution intensity of the three typical sampling places ranked as estuary of Nanfeihe River (NFH) > Zhongmiao Town (HZ) > Hongshizui (HSZ). Totally 129 phyla, 2631 genera and 12989 species were detected in the sediment samples, and HSZ, HZ and NFH had 35, 51 and 67 exclusive genera, respectively. The bacterial biomass and virus quantity from NFH accounted for 22.84% and 70.69% of total quantities, respectively, and the microbial community compositions in NFH were also different from those in HSZ and HZ. Metagenomics sequencing and functional gene annotation showed NFH contained many functional genes related to nucleic acid transport and metabolism, ribosome structures and biological origin, replication recombining and repair and inorganic ion transport and metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested the sediments from NFH were rich in enzymes correlated with heavy metal transport and reduction. Our findings offer some scientific basis for Chaohu Lake control and microbe resource utilization.}, }
@article {pmid34889667, year = {2021}, author = {Kang, S and Kim, KT and Choi, J and Kim, H and Cheong, K and Bandara, AY and Lee, YH}, title = {Genomics and informatics, conjoined tools vital for understanding and protecting plant health.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-10-21-0418-RVW}, pmid = {34889667}, issn = {0031-949X}, abstract = {Genomics' impact on crop production continuously expands. The number of sequenced plant and microbial species and strains representing diverse populations of individual species rapidly increases thanks to the advent of next generation sequencing technologies. Their genomic blueprints revealed candidate genes involved in various functions and processes crucial for crop health and helped understand how the sequenced organisms have evolved at the genome level. Functional genomics quickly translates these blueprints into a detailed mechanistic understanding of how such functions and processes work and are regulated; this understanding guides and empowers efforts to protect crops from diverse biotic and abiotic threats. Metagenome analyses help identify candidate microbes crucial for crop health and uncover how microbial communities associated with crop production respond to environmental conditions and cultural practices, presenting opportunities to enhance crop health by judiciously configuring microbial communities. Efficient conversion of disparate types of massive genomics data into actionable knowledge requires a robust informatics infrastructure supporting data preservation, analysis, and sharing. This review starts with an overview of how genomics came about and has quickly transformed life science. We illuminate how genomics and informatics can be applied to investigate various crop health-related problems using selected studies. We end the review by noting why community empowerment via crowdsourcing is crucial to harnessing genomics to protect global food and nutrition security without continuously expanding the environmental footprint of crop production.}, }
@article {pmid34889238, year = {2021}, author = {Zhang, M and Wang, W and Li, X and Zhang, X and Yang, D}, title = {Fast and precise pathogen detection and identification of overlapping infection in patients with CUTI based on metagenomic next-generation sequencing: A case report.}, journal = {Medicine}, volume = {100}, number = {49}, pages = {e27902}, doi = {10.1097/MD.0000000000027902}, pmid = {34889238}, issn = {1536-5964}, abstract = {RATIONALE: The gold standard for pathogen detection and identification of complicated urinary tract infection (CUTI) remains quantitative urine culture, however, the diagnostic value of urine culture remains limited due to the time-consuming procedure and low detection rate. Here we report a case of successfully using Metagenomic next-generation sequencing (mNGS) provided fast and precise detection and identification of overlapping infection in patients with CUTI with no similar reports or studies published before to the best of our knowledge.<br><br>PATIENT CONCERNS: A 70-year-old male was admitted to hospital due to elevated serum creatinine for 2 weeks.<br><br>DIAGNOSES: Acute exacerbation of chronic renal failure and CUTI were the most critical diagnosis on admission.<br><br>INTERVENTIONS: Blood purification, bladder irrigation and aggressive anti-infective therapy were administered. But the empirical anti-infection therapy and the adjustment of treatment according to the evidence of urine culture drug sensitivity had no obvious effect. We further carried out urinary PMseq-DNA detection and the results showed overlapping infection with Enterococcus faecium, Enterococcus hirae, Pseudomonas aeruginosa, Pseudomonas denitrificans and Candida albicans. According to the genetic test results, linezolid, meropenem and fluconazole triple anti-infection treatment was given.<br><br>OUTCOMES: After adjusting the treatment, the infection was basically controlled in 10 days, and even the renal function was significantly improved, dialysis independence was achieved after 3 months.<br><br>LESSONS: Our case illustrated the potential application of mNGS in detecting pathogenic microorganisms in patients with CUTI especially when overlapping infections are present.}, }
@article {pmid34888376, year = {2021}, author = {Ji, C and Jiang, J and Wei, Y and Wang, Z and Chen, Y and Mai, Z and Cai, M and Qin, C and Cai, Y and Yi, H and Liang, G and Lu, G and Gong, L and Zhang, G and Wang, H}, title = {A Method for the Analysis of African Swine Fever by Viral Metagenomic Sequencing.}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {766533}, pmid = {34888376}, issn = {2297-1769}, abstract = {In 2018, there was an outbreak of African swine fever (ASF) in China, which spread to other provinces in the following 3 years and severely damaged China's pig industry. ASF is caused by the African swine fever virus (ASFV). Given that the genome of the African swine fever virus is very complex and whole genome information is currently inadequate, it is important to efficiently obtain virus genome sequences for genomic and epidemiological studies. The prevalent ASFV strains have low genetic variability; therefore, whole genome sequencing analysis provides a basis for the study of ASFV. We provide a method for the efficient sequencing of whole genomes, which requires only a small number of tissues. The database construction method was selected according to the genomic types of ASFV, and the whole ASFV genome was obtained through data filtering, host sequence removal, virus classification, data assembly, virus sequence identification, statistical analysis, gene prediction, and functional analysis. Our proposed method will facilitate ASFV genome sequencing and novel virus discovery.}, }
@article {pmid34888258, year = {2021}, author = {Zhang, T and Zhang, S and Jin, C and Lin, Z and Deng, T and Xie, X and Deng, L and Li, X and Ma, J and Ding, X and Liu, Y and Shan, Y and Yu, Z and Wang, Y and Chen, G and Li, J}, title = {A Predictive Model Based on the Gut Microbiota Improves the Diagnostic Effect in Patients With Cholangiocarcinoma.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {751795}, pmid = {34888258}, issn = {2235-2988}, abstract = {Cholangiocarcinoma (CCA) is a malignant hepatic tumor with a poor prognosis, which needs early diagnosis urgently. The gut microbiota has been shown to play a crucial role in the progression of liver cancer. Here, we explored a gut microbiota model covering genera Burkholderia-Caballeronia-Paraburkholderia, Faecalibacterium, and Ruminococcus_1 (B-F-R) for CCA early diagnosis. A case-control study was conducted to enroll 53 CCA patients, 47 cholelithiasis patients, and 40 healthy controls. The feces samples and clinical information of participants were collected in the same period. The gut microbiota and its diversity of individuals were accessed with 16S rDNA sequencing, and the gut microbiota profile was evaluated according to microbiota diversity. Finally, four enriched genera in the CCA group (genera Bacteroides, Muribaculaceae_unclassified, Muribaculum, and Alistipes) and eight enriched genera in the cholelithiasis group (genera Bifidobacterium, Streptococcus, Agathobacter, Ruminococcus_gnavus_group, Faecalibacterium, Subdoligranulum, Collinsella, Escherichia-Shigella) constitute an overall different microbial community composition (P = 0.001). The B-F-R genera model with better diagnostic value than carbohydrate antigen 19-9 (CA19-9) was identified by random forest and Statistical Analysis of Metagenomic Profiles (STAMP) to distinguish CCA patients from healthy controls [area under the curve (AUC) = 0.973, 95% CI = 0.932-1.0]. Moreover, the correlative analysis found that genera Burkholderia-Caballeronia-Paraburkholderia were positively correlated with body mass index (BMI). The significantly different microbiomes between cholelithiasis and CCA were found via principal coordinates analysis (PCoA) and linear discriminant analysis effect size (LEfSe), and Venn diagram and LEfSe were utilized to identify four genera by comparing microbial compositions among patients with malignant obstructive jaundice (MOJ-Y) or not (MOJ-N). In brief, our findings suggest that gut microbiota vary from benign and malignant hepatobiliary diseases to healthy people and provide evidence supporting gut microbiota to be a non-invasive biomarker for the early diagnosis of CCA.}, }
@article {pmid34887842, year = {2021}, author = {Sengupta, A and Volkmann, THM and Danczak, RE and Stegen, JC and Dontsova, K and Abramson, N and Bugaj, AS and Volk, MJ and Matos, KA and Meira-Neto, AA and Barberán, A and Neilson, JW and Maier, RM and Chorover, J and Troch, PA and Meredith, LK}, title = {Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {754698}, pmid = {34887842}, issn = {1664-302X}, abstract = {Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.}, }
@article {pmid34887548, year = {2021}, author = {Conrad, RE and Viver, T and Gago, JF and Hatt, JK and Venter, SN and Rossello-Mora, R and Konstantinidis, KT}, title = {Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {34887548}, issn = {1751-7370}, support = {1831582//National Science Foundation (NSF)/ ; 1759831//National Science Foundation (NSF)/ ; }, abstract = {Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological processes that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of this ecosystem. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (~15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (noncore) genes were isolate-specific and showed low in situ abundances based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or transient, 3.5% of them became abundant when salinity (but not light) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results provide an explanation for how this immense intrapopulation gene diversity is maintained, which has implications for the prokaryotic species concept.}, }
@article {pmid34887434, year = {2021}, author = {Goswami, K and Shope, AJ and Tokarev, V and Wright, JR and Unverdorben, LV and Ly, T and Chen See, J and McLimans, CJ and Wong, HT and Lock, L and Clarkson, S and Parvizi, J and Lamendella, R}, title = {Comparative meta-omics for identifying pathogens associated with prosthetic joint infection.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23749}, pmid = {34887434}, issn = {2045-2322}, abstract = {Prosthetic joint infections (PJI) are economically and personally costly, and their incidence has been increasing in the United States. Herein, we compared 16S rRNA amplicon sequencing (16S), shotgun metagenomics (MG) and metatranscriptomics (MT) in identifying pathogens causing PJI. Samples were collected from 30 patients, including 10 patients undergoing revision arthroplasty for infection, 10 patients receiving revision for aseptic failure, and 10 patients undergoing primary total joint arthroplasty. Synovial fluid and peripheral blood samples from the patients were obtained at time of surgery. Analysis revealed distinct microbial communities between primary, aseptic, and infected samples using MG, MT, (PERMANOVA p = 0.001), and 16S sequencing (PERMANOVA p < 0.01). MG and MT had higher concordance with culture (83%) compared to 0% concordance of 16S results. Supervised learning methods revealed MT datasets most clearly differentiated infected, primary, and aseptic sample groups. MT data also revealed more antibiotic resistance genes, with improved concordance results compared to MG. These data suggest that a differential and underlying microbial ecology exists within uninfected and infected joints. This study represents the first application of RNA-based sequencing (MT). Further work on larger cohorts will provide opportunities to employ deep learning approaches to improve accuracy, predictive power, and clinical utility.}, }
@article {pmid34886820, year = {2021}, author = {Wigand, J and Tansirichaiya, S and Winje, E and Al-Haroni, M}, title = {Functional screening of a human saliva metagenomic DNA reveal novel resistance genes against sodium hypochlorite and chlorhexidine.}, journal = {BMC oral health}, volume = {21}, number = {1}, pages = {632}, pmid = {34886820}, issn = {1472-6831}, abstract = {OBJECTIVE: Many sections of the health care system are facing a major challenge making infectious disease problematic to treat; antimicrobial resistance (AMR). Identification and surveillance of the resistome have been highlighted as one of the strategies to overcome the problem. This study aimed to screen for AMR genes in an oral microbiota, a complex microbial system continuously exposed to antimicrobial agents commonly used in dental practice.<br><br>MATERIALS AND METHODS: As a significant part of the oral microbiome cannot be conventionally cultured, a functional metagenomic approach was chosen. The human oral metagenomic DNA was extracted from saliva samples collected from 50 healthy volunteers in Norway. The oral metagenomic library was then constructed by ligating partially digested oral metagenome into pSMART BAC vector and introducing into Escherichia coli. The library was screened against antimicrobials in dental practices. All resistant clones were selected and analyzed.<br><br>RESULTS: Screening of the oral metagenomic library against different antimicrobials detected multiple clones with resistance against chlorhexidine, triclosan, erythromycin, tetracycline, and sodium hypochlorite. Bioinformatic analysis revealed both already known resistance genes, including msr, mef(A), tetAB(46), and fabK, and genes that were not previously described to confer resistance, including recA and accB conferring resistance to sodium hypochlorite and chlorhexidine, respectively.<br><br>CONCLUSION: Multiple clones conferring resistance to antimicrobials commonly used in dental practices were detected, containing known and novel resistant genes by functional-based metagenomics. There is a need for more studies to increase our knowledge in the field.}, }
@article {pmid34885912, year = {2021}, author = {Marfil-Santana, MD and Martínez-Cárdenas, A and Ruíz-Hernández, A and Vidal-Torres, M and Márquez-Velázquez, NA and Figueroa, M and Prieto-Davó, A}, title = {A Meta-Omics Analysis Unveils the Shift in Microbial Community Structures and Metabolomics Profiles in Mangrove Sediments Treated with a Selective Actinobacterial Isolation Procedure.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {23}, pages = {}, doi = {10.3390/molecules26237332}, pmid = {34885912}, issn = {1420-3049}, support = {UNAM-DGAPA-PAPIIT TA200415//National Autonomous University of Mexico/ ; UNAM-DGAPA-PAPIIT IN222220//National Autonomous University of Mexico/ ; Proyecto Semilla FQ//National Autonomous University of Mexico/ ; }, abstract = {Mangrove sediment ecosystems in the coastal areas of the Yucatan peninsula are unique environments, influenced by their karstic origin and connection with the world's largest underground river. The microbial communities residing in these sediments are influenced by the presence of mangrove roots and the trading chemistry for communication between sediment bacteria and plant roots can be targeted for secondary metabolite research. To explore the secondary metabolite production potential of microbial community members in mangrove sediments at the "El Palmar" natural reserve in Sisal, Yucatan, a combined meta-omics approach was applied. The effects of a cultivation medium reported to select for actinomycetes within mangrove sediments' microbial communities was also analyzed. The metabolome of the microbial communities was analyzed by high-resolution liquid chromatography-tandem mass spectrometry, and molecular networking analysis was used to investigate if known natural products and their variants were present. Metagenomic results suggest that the sediments from "El Palmar" harbor a stable bacterial community independently of their distance from mangrove tree roots. An unexpected decrease in the observed abundance of actinomycetes present in the communities occurred when an antibiotic-amended medium considered to be actinomycete-selective was applied for a 30-day period. However, the use of this antibiotic-amended medium also enhanced production of secondary metabolites within the microbial community present relative to the water control, suggesting the treatment selected for antibiotic-resistant bacteria capable of producing a higher number of secondary metabolites. Secondary metabolite mining of "El Palmar" microbial community metagenomes identified polyketide synthase and non-ribosomal peptide synthetases' biosynthetic genes in all analyzed metagenomes. The presence of these genes correlated with the annotation of several secondary metabolites from the Global Natural Product Social Molecular Networking database. These results highlight the biotechnological potential of the microbial communities from "El Palmar", and show the impact selective media had on the composition of communities of actinobacteria.}, }
@article {pmid34884735, year = {2021}, author = {Hernandez-Baixauli, J and Puigbò, P and Abasolo, N and Palacios-Jordan, H and Foguet-Romero, E and Suñol, D and Galofré, M and Caimari, A and Baselga-Escudero, L and Bas, JMD and Mulero, M}, title = {Alterations in Metabolome and Microbiome Associated with an Early Stress Stage in Male Wistar Rats: A Multi-Omics Approach.}, journal = {International journal of molecular sciences}, volume = {22}, number = {23}, pages = {}, doi = {10.3390/ijms222312931}, pmid = {34884735}, issn = {1422-0067}, abstract = {Stress disorders have dramatically increased in recent decades becoming the most prevalent psychiatric disorder in the United States and Europe. However, the diagnosis of stress disorders is currently based on symptom checklist and psychological questionnaires, thus making the identification of candidate biomarkers necessary to gain better insights into this pathology and its related metabolic alterations. Regarding the identification of potential biomarkers, omic profiling and metabolic footprint arise as promising approaches to recognize early biochemical changes in such disease and provide opportunities for the development of integrative candidate biomarkers. Here, we studied plasma and urine metabolites together with metagenomics in a 3 days Chronic Unpredictable Mild Stress (3d CUMS) animal approach that aims to focus on the early stress period of a well-established depression model. The multi-omics integration showed a profile composed by a signature of eight plasma metabolites, six urine metabolites and five microbes. Specifically, threonic acid, malic acid, alpha-ketoglutarate, succinic acid and cholesterol were proposed as key metabolites that could serve as key potential biomarkers in plasma metabolome of early stages of stress. Such findings targeted the threonic acid metabolism and the tricarboxylic acid (TCA) cycle as important pathways in early stress. Additionally, an increase in opportunistic microbes as virus of the Herpesvirales was observed in the microbiota as an effect of the primary stress stages. Our results provide an experimental biochemical characterization of the early stage of CUMS accompanied by a subsequent omic profiling and a metabolic footprinting that provide potential candidate biomarkers.}, }
@article {pmid34883258, year = {2021}, author = {Liu, X and Shen, M and Yan, H and Long, P and Jiang, H and Zhang, Y and Zhou, L and Yu, K and Qiu, G and Yang, H and Li, X and Min, X and He, M and Zhang, X and Choi, H and Wang, C and Wu, T}, title = {Alternations in the gut microbiota and metabolome with newly diagnosed unstable angina.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2021.11.009}, pmid = {34883258}, issn = {1673-8527}, abstract = {Gut microbiota plays an important role in coronary heart disease, but its compositional and functional changes in unstable angina (UA) remain unexplored. We performed metagenomic sequencing of 133 newly diagnosed UA patients and 133 sex- and age-matched controls, and profiled the fecal and plasma metabolomes in thirty case-control pairs. The alpha diversity of gut microbiota was increased in UA patients: the adjusted odds ratios (ORs) per standard deviation increase in Shannon and Simpson indices were 1.30 (95% confidence interval, 1.01-1.70) and 1.36 (1.05-1.81), respectively. Two common species (depleted Klebsiella pneumoniae and enriched Streptococcus parasanguinis; P ≤ 0.002) and three rare species (depleted Weissella confusa, enriched Granulicatella adiacens and Erysipelotrichaceae bacterium 6_1_45; P ≤ 0.005) were associated with UA. The UA-associated gut microbiota was depleted in the pathway of L-phenylalanine degradation (P = 0.001), primarily contributed by Klebsiella pneumoniae. Consistently, we found increased circulating phenylalanine in UA patients (OR = 2.76 [1.17-8.16]). Moreover, S. parasanguinis was negatively correlated with fecal citrulline (Spearman's rs = -0.470, P = 0.009), a metabolite depleted in UA patients (OR = 0.26 [0.08-0.63]). These findings are informative to help understand the metabolic connection between gut microbiota and UA.}, }
@article {pmid34882767, year = {2021}, author = {Kiguchi, Y and Nishijima, S and Kumar, N and Hattori, M and Suda, W}, title = {Erratum to: Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {28}, number = {6}, pages = {}, doi = {10.1093/dnares/dsab025}, pmid = {34882767}, issn = {1756-1663}, }
@article {pmid34882353, year = {2021}, author = {Balmasova, IP and Tsarev, VN and Unanyan, KG and Ippolitov, EV and Tsareva, TV and Kharakh, YN and Akhmedov, GD and Stepanova, SY and Katkov, II and Arutyunov, SD}, title = {Diagnostic value of microbiome biomarkers of the periodonite microbiome in patients with the association of chronic periodontitis and diabetes mellitus type 2.}, journal = {Klinicheskaia laboratornaia diagnostika}, volume = {66}, number = {11}, pages = {678-683}, doi = {10.51620/0869-2084-2021-66-11-678-683}, pmid = {34882353}, issn = {0869-2084}, abstract = {The place of high-tech methods of molecular biology in clinical laboratory diagnostics of various diseases and the development of a system of biomarkers as an important component of diagnostic research is currently attracting the closest attention of the scientific community. In this paper, an attempt is made to use high-tech metagenomic analysis to solve problems that arise due to the high frequency of association of periodontal diseases with systemic pathology, in particular, with type 2 diabetes mellitus. The aim of the study was to determine the taxonomic and metabolic features of the microbiome of periodontal tissues in periodontal diseases associated with type 2 diabetes mellitus, as a model of the ratio of local and systemic effects of periodontal pathogenic bacteria. The study included 16S shotgun sequencing of bacterial DNA as part of biological material from periodontal pockets/dentoalveolar furrows of 46 people - 15 patients with chronic periodontitis associated with type 2 diabetes mellitus, 15 patients with chronic periodontitis unrelated to systemic pathology, as well as 16 healthy people in the control group, followed by bioinformatic processing of the data obtained. The obtained data allowed us to establish the taxonomic features of the periodontal microbiome in the association of chronic periodontitis with type 2 diabetes mellitus, which included the predominance of representatives of the families Prevotellaceae and Spirochaetaceae in its composition. The features of metabolic processes in periodontal tissues with the participation of the microbiome were also revealed, which consisted in an increase in the exchange of cysteine and methionine against the background of a decrease in the metabolism of pyrimidine, methane, sphingolipids, and the synthesis of fatty acids, which are of diagnostic value in assessing the condition of patients with type 2 diabetes mellitus.}, }
@article {pmid34881320, year = {2021}, author = {Takhampunya, R and Sakolvaree, J and Chanarat, N and Youngdech, N and Phonjatturas, K and Promsathaporn, S and Tippayachai, B and Tachavarong, W and Srinoppawan, K and Poole-Smith, BK and McCardle, PW and Chaorattanakawee, S}, title = {The Bacterial Community in Questing Ticks From Khao Yai National Park in Thailand.}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {764763}, pmid = {34881320}, issn = {2297-1769}, abstract = {Ticks are known vectors for a variety of pathogens including bacteria, viruses, fungi, and parasites. In this study, bacterial communities were investigated in active life stages of three tick genera (Haemaphysalis, Dermacentor, and Amblyomma) collected from Khao Yai National Park in Thailand. Four hundred and thirty-three questing ticks were selected for pathogen detection individually using real-time PCR assays, and 58 of these were subjected to further metagenomics analysis. A total of 62 ticks were found to be infected with pathogenic bacteria, for a 14.3% prevalence rate, with Amblyomma spp. exhibiting the highest infection rate (20.5%), followed by Haemaphysalis spp. (14.5%) and Dermacentor spp. (8.6%). Rickettsia spp. were the most prevalent bacteria (7.9%) found, followed by Ehrlichia spp. (3.2%), and Anaplasma spp. and Borrelia spp. each with a similar prevalence of 1.6%. Co-infection between pathogenic bacteria was only detected in three Haemaphysalis females, and all co-infections were between Rickettsia spp. and Anaplasmataceae (Ehrlichia spp. or Anaplasma spp.), accounting for 4.6% of infected ticks or 0.7% of all examined questing ticks. The prevalence of the Coxiella-like endosymbiont was also investigated. Of ticks tested, 65.8% were positive for the Coxiella-like endosymbiont, with the highest infection rate in nymphs (86.7%), followed by females (83.4%). Among tick genera, Haemaphysalis exhibited the highest prevalence of infection with the Coxiella-like endosymbiont. Ticks harboring the Coxiella-like endosymbiont were more likely to be infected with Ehrlichia spp. or Rickettsia spp. than those without, with statistical significance for Ehrlichia spp. infection in particular (p-values = 0.003 and 0.917 for Ehrlichia spp. and Rickettsia spp., respectively). Profiling the bacterial community in ticks using metagenomics revealed distinct, predominant bacterial taxa in tick genera. Alpha and beta diversities analyses showed that the bacterial community diversity and composition in Haemaphysalis spp. was significantly different from Amblyomma spp. However, when examining bacterial diversity among tick life stages (larva, nymph, and adult) in Haemaphysalis spp., no significant difference among life stages was detected. These results provide valuable information on the bacterial community composition and co-infection rates in questing ticks in Thailand, with implications for animal and human health.}, }
@article {pmid34881191, year = {2021}, author = {Afolayan, AO and Biagi, E and Rampelli, S and Candela, M and Brigidi, P and Turroni, S and Ayeni, FA}, title = {The Gut Microbiota of an Individual Varies With Intercontinental Four-Month Stay Between Italy and Nigeria: A Pilot Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {725769}, pmid = {34881191}, issn = {2235-2988}, abstract = {Despite well-established knowledge of the role of diet and the geographic effect on the gut microbiota of human populations, the temporal dynamics of the individual microbiota profile across changes associated with intercontinental short residence are still far from being understood. This pilot study sought to provide insights into the trajectory of the gut microbiota of an individual during a two-month stay in Italy and a subsequent two-month stay in Nigeria, by 16S rRNA gene sequencing and inferred metagenomics. The gut microbiota underwent massive but temporary changes, both taxonomically and based on predicted functionality. The faecal microbiota associated with the short stay in Italy progressively lost diversity and showed a dominance of Firmicutes, while after returning to Nigeria, the microbial community quickly regained the typical profile, in terms of biodiversity and bacterial signatures of traditional lifestyle, i.e., Prevotella and Treponema. Predicted pathways involved in glycolysis, fermentation and N-acetylneuraminate degradation were enriched during the subsequent two-month stay in Nigeria, whereas pathways associated with amino acid and peptidoglycan synthesis and maturation became over-represented during short stay in Italy. Our findings stress the plasticity of the individual gut microbiota even during a short-term travel, with loss/gain of taxonomic and functional features that mirror those of the gut microbiota of indigenous people dwelling therein.}, }
@article {pmid34880836, year = {2021}, author = {Wu, CY and Meng, J and Merchant, A and Zhang, YX and Li, MW and Zhou, XG and Wang, Q}, title = {Microbial Response to Fungal Infection in a Fungus-Growing Termite, Odontotermes formosanus (Shiraki).}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {723508}, pmid = {34880836}, issn = {1664-302X}, abstract = {The crosstalk between gut microbiota and host immunity has emerged as one of the research foci of microbiome studies in recent years. The purpose of this study was to determine how gut microbes respond to fungal infection in termites, given their reliance on gut symbionts for food intake as well as maintaining host health. Here, we used Metarhizium robertsii, an entomopathogenic fungus, to infect Odontotermes formosanus, a fungus-growing termite in the family Termitidae, and documented changes in host gut microbiota via a combination of bacterial 16S rDNA sequencing, metagenomic shotgun sequencing, and transmission electron microscopy. Our analyses found that when challenged with Metarhizium, the termite gut showed reduced microbial diversity within the first 12 h of fungal infection and then recovered and even surpassed pre-infection flora levels. These combined results shed light on the role of gut flora in maintaining homeostasis and immune homeostasis in the host, and the impact of gut flora dysbiosis on host susceptibility to infection.}, }
@article {pmid34880054, year = {2021}, author = {Tomofuji, Y and Kishikawa, T and Maeda, Y and Ogawa, K and Nii, T and Okuno, T and Oguro-Igashira, E and Kinoshita, M and Yamamoto, K and Sonehara, K and Yagita, M and Hosokawa, A and Motooka, D and Matsumoto, Y and Matsuoka, H and Yoshimura, M and Ohshima, S and Nakamura, S and Inohara, H and Mochizuki, H and Takeda, K and Kumanogoh, A and Okada, Y}, title = {Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease.}, journal = {Annals of the rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1136/annrheumdis-2021-221267}, pmid = {34880054}, issn = {1468-2060}, abstract = {OBJECTIVE: The relationship between autoimmune diseases and the gut microbiome has been intensively studied, and several autoimmunity-associated bacterial taxa have been identified. However, much less is known about the roles of the gut virome in autoimmune diseases.<br><br>METHODS: Here, we performed a whole gut virome analysis based on the shotgun sequencing of 476 Japanese which included patients with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), multiple sclerosis and healthy control subjects.<br><br>RESULTS: Our case-control comparison of the viral abundance revealed that crAss-like phages, which are one of the main components of a healthy gut virome, significantly decreased in the gut of the patients with autoimmune disease, specifically the patients with RA and SLE. In addition, Podoviridae significantly decreased in the gut of the patients with SLE. To understand how these viruses affected the bacteriome, we performed a quantitative virus-bacterium association analysis and clustered regularly interspaced short palindromic repeat-based virus-bacterium interaction analysis. We identified a symbiosis between Podoviridae and Faecalibacterium. In addition, multiple bacterial targets of crAss-like phages were identified (eg, Ruminococcus spp).<br><br>CONCLUSION: Our data suggest that the gut virome can affect our body either directly or via bacteria. Our analyses have elucidated a previously missing part of the autoimmunity-associated gut microbiome and presented new candidates that contribute to the development of autoimmune diseases.}, }
@article {pmid34879255, year = {2021}, author = {Quintão, TSC and Slavov, SN and de Oliveira, PM and Bezerra, RDS and Cassemiro, ÉM and Alves, PPM and Gontijo, CC and Martins, FDAP and Gurgel, HDC and Noronha, EF and Ramalho, WM and de Araújo, WN and Pereira, AL and Haddad, R}, title = {Viral metagenomics in nasopharyngeal swabs of Brazilian patients negative for SARS-CoV-2 unveils the presence of Chikungunya virus infection.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {}, pmid = {34879255}, issn = {1532-2742}, }
@article {pmid34878672, year = {2021}, author = {Wu, L and Yang, F and Feng, J and Tao, X and Qi, Q and Wang, C and Schuur, EAG and Bracho, R and Huang, Y and Cole, JR and Tiedje, JM and Zhou, J}, title = {Permafrost thaw with warming reduces microbial metabolic capacities in sub-surface soils.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16319}, pmid = {34878672}, issn = {1365-294X}, abstract = {Microorganisms are major constituents of the total biomass in permafrost regions, whose underlain soils are frozen for at least two consecutive years. To understand potential microbial responses to climate change, here we examined microbial community compositions and functional capacities across four soil depths in an Alaska tundra site. We showed that a 5-year warming treatment increased soil thaw depth by 25.7% (P = 0.011) within the deep organic layer (15 -25 cm). Concurrently, warming reduced 37% of bacterial abundance and 64% of fungal abundances in the deep organic layer, while it did not affect microbial abundance in other soil layers (i.e., 0 - 5 cm, 5 - 15 cm, and 45 - 55 cm). Warming treatment altered fungal community composition and microbial functional structure (P < 0.050), but not bacterial community composition. Using a functional gene array, we found that the relative abundances of a variety of carbon (C)-decomposing, iron-reducing, and sulfate-reducing genes in the deep organic layer were decreased, which was not observed by the shotgun sequencing-based metagenomics analysis of those samples. To explain the reduced metabolic capacities, we found that warming treatment elicited higher deterministic environmental filtering, which could be linked to water-saturated time, soil moisture, and soil thaw duration. In contrast, plant factors showed little influence on microbial communities in sub-surface soils below 15 cm, despite a 25.2% higher (P < 0.05) aboveground plant biomass by warming treatment. Collectively, we demonstrate that microbial metabolic capacities in sub-surface soils are reduced, likely arising from enhanced thaw by warming.}, }
@article {pmid34878610, year = {2021}, author = {Kumar, V and Kumar, S and Singh, D}, title = {Metagenomic insights into Himalayan glacial and kettle lake sediments revealed microbial community structure, function, and stress adaptation strategies.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {1}, pages = {3}, pmid = {34878610}, issn = {1433-4909}, support = {MLP0143//CSIR-Institute of Himalayan Bioresource Technology/ ; }, abstract = {Glacial and kettle lakes in the high-altitude Himalayas are unique habitats with significant scope for microbial ecology. The present study provides insights into bacterial community structure and function of the sediments of two high-altitude lakes using 16S amplicon and whole-genome shotgun (WGS) metagenomics. Microbial communities in the sediments of Parvati kund (glacial lake) and Bhoot ground (kettle lake) majorly consist of bacteria and a small fraction of archaea and eukaryota. The bacterial population has an abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. Despite the common phyla, the sediments from each lake have a distinct distribution of bacterial and archaeal taxa. The analysis of the WGS metagenomes at the functional level provides a broad picture of microbial community metabolism of key elements and suggested chemotrophs as the major primary producers. In addition, the findings also revealed that polyhydroxyalkanoates (PHA) are a crucial stress adaptation molecule. The abundance of PHA metabolism in Alpha- and Betaproteobacteria and less representation in other bacterial and archaeal classes in both metagenomes was disclosed. The metagenomic insights provided an incisive view of the microbiome from Himalayan lake's sediments. It has also opened the scope for further bioprospection from virgin Himalayan niches.}, }
@article {pmid34878325, year = {2021}, author = {Li, J and Zheng, X and Li, L and Zhang, S and Ren, M and Huang, L and Dong, X}, title = {The Archaeal Transcription Termination Factor aCPSF1 is a Robust Phylogenetic Marker for Archaeal Taxonomy.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0153921}, doi = {10.1128/spectrum.01539-21}, pmid = {34878325}, issn = {2165-0497}, abstract = {Archaea are highly diverse and represent a primary life domain, but the majority of them remain uncultured. Currently, 16S rRNA phylogeny is widely used in archaeal taxonomy and diversity surveys. However, highly conserved sequence of 16S rRNA possibly results in generation of chimera in the amplicons and metagenome-assembled genomes (MAGs) and therefore limits its application. The newly developed phylogenomic approach has overcome these flaws, but it demands high-quality MAGs and intensive computation. In this study, we investigated the use of the archaeal transcription termination factor aCPSF1 in archaeal classification and diversity surveys. The phylogenetic analysis of 1,964 aCPSF1 orthologs retrieved from the available archaeal (meta)genomes resulted in convergent clustering patterns with those of archaeal phylogenomics and 16S rRNA phylogeny. The aCPSF1 phylogeny also displayed comparable clustering with the methanoarchaeal McrABG phylogeny and the haloarchaeal phylogenomics. Normalization of 779 aCPSF1 sequences including 261 from cultured archaeal species yielded a taxonomic ranking system with higher resolutions than that obtained with 16S rRNA for genus and species. Using the aCPSF1 taxonomy, 144 unclassified archaea in NCBI database were identified to various taxonomic ranks. Moreover, aCPSF1- and 16S rRNA-based surveys of the archaeal diversity in a sample from a South China Sea cold seep produced similar results. Our results demonstrate that aCPSF1 is an alternative archaeal phylogenetic marker, which exhibits higher resolution than 16S rRNA, and is more readily usable than phylogenomics in the taxonomic study of archaea. IMPORTANCE Archaea represent a unique type of prokaryote, which inhabit in various environments including extreme environments, and so define the boundary of biosphere, and play pivotal ecological roles, particularly in extreme environments. Since their discovery over 40 years ago, environmental archaea have been widely investigated using the 16S rRNA sequence comparison, and the recently developed phylogenomic approach because the majority of archaea are recalcitrant to laboratory cultivation. However, the highly conserved sequence of 16S rRNA and intensive bioinformatic computation of phylogenomics limit their applications in archaeal species delineation and diversity investigations. aCPSF1 is a ubiquitously distributed and vertically inherited transcription termination factor in archaea. In this study, we developed an aCPSF1-based archaeal taxonomic system which exhibits congruent phylogenic clustering patterns with archaeal phylogenomics and higher resolution than 16S rRNA in distinguishing archaea at lower taxonomic ranks. Therefore, aCPSF1 is a new phylogenetic marker in the taxonomic and diversity studies of archaea.}, }
@article {pmid34877329, year = {2021}, author = {Lin, ZN and Sun, YC and Wang, JP and Lai, YL and Sheng, LX}, title = {Next-generation sequencing technology for diagnosis and efficacy evaluation of a patient with visceral leishmaniasis: A case report.}, journal = {World journal of clinical cases}, volume = {9}, number = {32}, pages = {9903-9910}, pmid = {34877329}, issn = {2307-8960}, abstract = {BACKGROUND: Visceral leishmaniasis (VL) is a parasitic disease caused by Leishmania and transmitted by infected sand flies. VL has a low incidence in China, and its clinical presentation is complex and atypical. This disease is easily misdiagnosed and can become life-threatening within a short period of time. Therefore, early, rapid and accurate diagnosis and treatment of the disease are essential.<br><br>CASE SUMMARY: A 25-year-old male patient presented with the clinical manifestations of irregular fever, hepatosplenomegaly, increased polyclonal globulin, and pancytopenia. The first bone marrow puncture biopsy did not provide a clear diagnosis. In order to relieve the pressure and discomfort of the organs caused by the enlarged spleen and to confirm the diagnosis, splenectomy was performed, and hemophagocytic syndrome was diagnosed by pathological examination of the spleen biopsy. Following bone marrow and spleen pathological re-diagnosis and metagenomic next-generation sequencing (mNGS) technology detection, the patient was finally diagnosed with VL. After treatment with liposomal amphotericin B, the body temperature quickly returned to normal and the hemocytes recovered gradually. Post-treatment re-examination of the bone marrow puncture and mNGS data showed that Leishmania was not detected.<br><br>CONCLUSION: As a fast and accurate detection method, mNGS can diagnose and evaluate the efficacy of treatment in suspicious cases of leishmaniasis.}, }
@article {pmid34877302, year = {2021}, author = {Gu, LY and Tian, J and Yan, YP}, title = {Concurrent tuberculous transverse myelitis and asymptomatic neurosyphilis: A case report.}, journal = {World journal of clinical cases}, volume = {9}, number = {31}, pages = {9645-9651}, pmid = {34877302}, issn = {2307-8960}, abstract = {BACKGROUND: Tuberculous myelitis is a rare manifestation of tuberculosis (TB) that is usually caused by hematogenous spread of Mycobacterium tuberculosis (MTB). Neurosyphilis is a neurological disease that occurs when Treponema pallidum invades the brain or the spinal cord. Individually, these two diseases involving the spinal cord are rare and cases of concurrent tuberculous transverse myelitis and asymptomatic neurosyphilis have seldom been reported.<br><br>CASE SUMMARY: A 56-year-old man presented with numbness and pain of both lower limbs for 2 wk and dysuria for 1 wk. Syphilis serology and cerebrospinal fluid (CSF) analysis supported the diagnosis of neurosyphilis and the patient was treated with intravenous ceftriaxone at first, but symptoms still progressed. Then, magnetic resonance images revealed multiple lesions along the cervicothoracic junction, and chest computed tomography showed a typical TB lesion. MTB DNA was detected in the CSF sample by metagenomic next-generation sequencing. Eventually the patient was diagnosed with tuberculous myelitis combined with asymptomatic neurosyphilis. Subsequently, quadruple anti-TB drug standardized therapy was empirically used and his neurological symptoms improved gradually.<br><br>CONCLUSION: Patients can have coinfection with tuberculous transverse myelitis and asymptomatic neurosyphilis. Patients with neurosyphilis should be examined for other pathogens.}, }
@article {pmid34876830, year = {2021}, author = {Danilenko, V and Devyatkin, A and Marsova, M and Shibilova, M and Ilyasov, R and Shmyrev, V}, title = {Common Inflammatory Mechanisms in COVID-19 and Parkinson's Diseases: The Role of Microbiome, Pharmabiotics and Postbiotics in Their Prevention.}, journal = {Journal of inflammation research}, volume = {14}, number = {}, pages = {6349-6381}, pmid = {34876830}, issn = {1178-7031}, abstract = {In the last decade, metagenomic studies have shown the key role of the gut microbiome in maintaining immune and neuroendocrine systems. Malfunction of the gut microbiome can induce inflammatory processes, oxidative stress, and cytokine storm. Dysfunction of the gut microbiome can be caused by short-term (virus infection and other infectious diseases) or long-term (environment, nutrition, and stress) factors. Here, we reviewed the inflammation and oxidative stress in neurodegenerative diseases and coronavirus infection (COVID-19). Here, we reviewed the renin-angiotensin-aldosterone system (RAAS) involved in the processes of formation of oxidative stress and inflammation in viral and neurodegenerative diseases. Moreover, the coronavirus uses ACE2 receptors of the RAAS to penetrate human cells. The coronavirus infection can be the trigger for neurodegenerative diseases by dysfunction of the RAAS. Pharmabiotics, postbiotics, and next-generation probiotics, are considered as a means to prevent oxidative stress, inflammatory processes, neurodegenerative and viral diseases through gut microbiome regulation.}, }
@article {pmid34876793, year = {2021}, author = {Chung, MW and Kim, MJ and Won, EJ and Lee, YJ and Yun, YW and Cho, SB and Joo, YE and Hwang, JE and Bae, WK and Chung, IJ and Shin, MG and Shin, JH}, title = {Gut microbiome composition can predict the response to nivolumab in advanced hepatocellular carcinoma patients.}, journal = {World journal of gastroenterology}, volume = {27}, number = {42}, pages = {7340-7349}, pmid = {34876793}, issn = {2219-2840}, abstract = {BACKGROUND: Immunotherapy has revolutionized the clinical outcomes of intractable cancer patients. Little is known about the intestinal nonpathogenic bacterial composition of hepatocellular carcinoma (HCC) patients treated by immunotherapy.<br><br>AIM: To determine whether there is a correlation between gut bacterial composition and prognosis in HCC patients.<br><br>METHODS: From September 2019 to March 2020, we prospectively collected fecal samples and examined the gut microbiome of 8 advanced HCC patients treated with nivolumab as a second- or third-line systemic treatment. Fecal samples were collected before the start of immunotherapy. Fecal samples of patients with progression during treatment were collected at the time of progression, and fecal samples of patients who showed good response to nivolumab were collected after 5-7 mo as follow-up. Metagenomic data from 16S ribosomal RNA sequencing were analyzed using CLC Genomics Workbench. Microbiome data were analyzed according to therapeutic response.<br><br>RESULTS: All 8 patients were male, of which 6 had underlying chronic hepatitis B. A higher Shannon index was found in the responders than in the non-responders after nivolumab therapy (P = 0.036). The unweighted beta diversity analysis also showed that the overall bacterial community structure and phylogenetic diversity were clearly distinguished according to therapeutic response. There was no significant difference in the diversity or composition of the patient gut microbiome according to the immunotherapy used. Several taxa specific to therapeutic response were designated as follows: Dialister pneumosintes, Escherichia coli, Lactobacillus reteri, Streptococcus mutans, Enterococcus faecium, Streptococcus gordonii, Veillonella atypica, Granulicatella sp., and Trchuris trichiura for the non-responders; Citrobacter freundii, Azospirillum sp. and Enterococcus durans for the responders. Of note, a skewed Firmicutes/Bacteroidetes ratio and a low Prevotella/Bacteroides ratio can serve as predictive markers of non-response, whereas the presence of Akkermansia species predicts a good response.<br><br>CONCLUSION: The current presumptive study suggests a potential role for the gut microbiome as a prognostic marker for the response to nivolumab in treatment of HCC patients.}, }
@article {pmid34876683, year = {2021}, author = {Taubert, M and Overholt, WA and Heinze, BM and Matanfack, GA and Houhou, R and Jehmlich, N and von Bergen, M and Rösch, P and Popp, J and Küsel, K}, title = {Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {34876683}, issn = {1751-7370}, support = {218627073//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 218627073//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 218627073//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 218627073//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; MetaPro//Helmholtz-Zentrum für Umweltforschung (Helmholtz Centre for Environmental Research)/ ; MetaPro//Helmholtz-Zentrum für Umweltforschung (Helmholtz Centre for Environmental Research)/ ; }, abstract = {Current understanding of organic carbon inputs into ecosystems lacking photosynthetic primary production is predicated on data and inferences derived almost entirely from metagenomic analyses. The elevated abundances of putative chemolithoautotrophs in groundwaters suggest that dark CO2 fixation is an integral component of subsurface trophic webs. To understand the impact of autotrophically fixed carbon, the flux of CO2-derived carbon through various populations of subsurface microbiota must first be resolved, both quantitatively and temporally. Here we implement novel Stable Isotope Cluster Analysis to render a time-resolved and quantitative evaluation of 13CO2-derived carbon flow through a groundwater community in microcosms stimulated with reduced sulfur compounds. We demonstrate that mixotrophs, not strict autotrophs, were the most abundant active organisms in groundwater microcosms. Species of Hydrogenophaga, Polaromonas, Dechloromonas, and other metabolically versatile mixotrophs drove the production and remineralization of organic carbon. Their activity facilitated the replacement of 43% and 80% of total microbial carbon stores in the groundwater microcosms with 13C in just 21 and 70 days, respectively. The mixotrophs employed different strategies for satisfying their carbon requirements by balancing CO2 fixation and uptake of available organic compounds. These different strategies might provide fitness under nutrient-limited conditions, explaining the great abundances of mixotrophs in other oligotrophic habitats, such as the upper ocean and boreal lakes.}, }
@article {pmid34876615, year = {2021}, author = {Gao, B and Jose, A and Alonzo-Palma, N and Malik, T and Shankaranarayanan, D and Regunathan-Shenk, R and Raj, DS}, title = {Butyrate producing microbiota are reduced in chronic kidney diseases.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {23530}, pmid = {34876615}, issn = {2045-2322}, abstract = {Chronic kidney disease is a major public health concern that affects millions of people globally. Alterations in gut microbiota composition have been observed in patients with chronic kidney disease. Nevertheless, the correlation between the gut microbiota and disease severity has not been investigated. In this study, we performed shot-gun metagenomics sequencing and identified several taxonomic and functional signatures associated with disease severity in patients with chronic kidney disease. We noted that 19 microbial genera were significantly associated with the severity of chronic kidney disease. The butyrate-producing bacteria were reduced in patients with advanced stages of chronic kidney diseases. In addition, functional metagenomics showed that two-component systems, metabolic activity and regulation of co-factor were significantly associated with the disease severity. Our study provides valuable information for the development of microbiota-oriented therapeutic strategies for chronic kidney disease.}, }
@article {pmid34876586, year = {2021}, author = {Marushchak, ME and Kerttula, J and Diáková, K and Faguet, A and Gil, J and Grosse, G and Knoblauch, C and Lashchinskiy, N and Martikainen, PJ and Morgenstern, A and Nykamb, M and Ronkainen, JG and Siljanen, HMP and van Delden, L and Voigt, C and Zimov, N and Zimov, S and Biasi, C}, title = {Thawing Yedoma permafrost is a neglected nitrous oxide source.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {7107}, pmid = {34876586}, issn = {2041-1723}, support = {287469//Academy of Finland (Suomen Akatemia)/ ; 314630//Academy of Finland (Suomen Akatemia)/ ; 337550//Academy of Finland (Suomen Akatemia)/ ; 317054//Academy of Finland (Suomen Akatemia)/ ; 290315//Academy of Finland (Suomen Akatemia)/ ; 342362//Academy of Finland (Suomen Akatemia)/ ; 332196//Academy of Finland (Suomen Akatemia)/ ; 18-55-11003 AF_t//Russian Foundation for Basic Research (RFBR)/ ; 18-55-11003 AF_t//Russian Foundation for Basic Research (RFBR)/ ; 03G0836A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0834B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, abstract = {In contrast to the well-recognized permafrost carbon (C) feedback to climate change, the fate of permafrost nitrogen (N) after thaw is poorly understood. According to mounting evidence, part of the N liberated from permafrost may be released to the atmosphere as the strong greenhouse gas (GHG) nitrous oxide (N2O). Here, we report post-thaw N2O release from late Pleistocene permafrost deposits called Yedoma, which store a substantial part of permafrost C and N and are highly vulnerable to thaw. While freshly thawed, unvegetated Yedoma in disturbed areas emit little N2O, emissions increase within few years after stabilization, drying and revegetation with grasses to high rates (548 (133-6286) μg N m-2 day-1; median with (range)), exceeding by 1-2 orders of magnitude the typical rates from permafrost-affected soils. Using targeted metagenomics of key N cycling genes, we link the increase in in situ N2O emissions with structural changes of the microbial community responsible for N cycling. Our results highlight the importance of extra N availability from thawing Yedoma permafrost, causing a positive climate feedback from the Arctic in the form of N2O emissions.}, }
@article {pmid34876042, year = {2021}, author = {Chen, M and Lu, W and Wu, S and Wang, S and Lu, T and Peng, C}, title = {Metagenomic next-generation sequencing in the diagnosis of leptospirosis presenting as severe diffuse alveolar hemorrhage: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {21}, number = {1}, pages = {1230}, pmid = {34876042}, issn = {1471-2334}, abstract = {BACKGROUND: Leptospirosis is a common infectious disease in tropical and semitropical regions, and it is typically neglected. Leptospirosis-associated acute diffuse alveolar hemorrhage is one of its fatal complications. The use of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing in the diagnosis of Leptospira interrogans infection has rarely been reported.<br><br>CASE PRESENTATION: We present the case of a 62-year-old female who was transferred to our hospital with dyspnea, and severe hemoptysis and was supported by a tracheal intubation ventilator. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) reported Leptospira interrogans. A diagnosis of diffuse alveolar hemorrhage caused by leptospirosis was made. After immediately receiving antibiotics and hormone therapy, the patient achieved a complete recovery upon discharge.<br><br>CONCLUSION: Leptospirosis presenting as severe diffuse alveolar hemorrhage is rare but should be considered in the differential diagnosis. mNGS can help identify pathogens and treat them early, which can improve prognosis.}, }
@article {pmid34876034, year = {2021}, author = {Liu, MF and Liu, Y and Xu, DR and Wan, LG and Zhao, R}, title = {mNGS helped diagnose scrub typhus presenting as a urinary tract infection with high D-dimer levels: a case report.}, journal = {BMC infectious diseases}, volume = {21}, number = {1}, pages = {1219}, pmid = {34876034}, issn = {1471-2334}, support = {20192BAB205088//Natural Science Foundation of Jiangxi Province/ ; 180120//Natural Science Foundation of Jiangxi Province Department of Education/ ; }, abstract = {BACKGROUND: Scrub typhus is caused by O. tsutsugamushi and spreads through mite larvae biting the skin. Classic symptoms of the disease are eschar and lymphadenopathy. Previous reports have revealed clinical manifestations of scrub typhus, including gastrointestinal symptoms, meningoencephalitis, ocular flutter, pneumonitis, acute respiratory distress syndrome, and acute kidney injury. However, cases of scrub typhus presenting as a urinary tract infection (UTI) with high D-dimer levels could be easily misdiagnosed when clinical attention is insufficient, resulting in difficulty in making a timely diagnosis of the infection. Metagenomics next-generation sequencing (mNGS) is a revolutionary and highly sensitive method that may help in diagnosing atypical cases, even when trace amounts of pathogens are present.<br><br>CASE PRESENTATION: A 52-year-old female presented with a 10-day history of fever, chills, headache and myalgia. She was initially diagnosed with influenza at a local clinic. Various antibacterials were used on the 2nd-12th day onwards; however, her symptoms persisted and were followed by increased urination duration, frequency, urgency and dysuria for 2 days. Orientia tsutsugamushi was confirmed as the pathogen responsible for the infection through mNGS analysis of her blood samples from Day 13 onwards. The patient's temperature changed remarkably 24 h after the initiation of doxycycline. Over the next 48 h (i.e., Day 15 onwards), the patient showed clinical improvement. She recovered and was discharged from the hospital.<br><br>CONCLUSIONS: Scrub typhus can present atypical clinical symptoms, such as UTIs, in a febrile patient. mNGS may be a useful method for identifying O. tsutsugamushi infection in patients with atypical clinical manifestations.}, }
@article {pmid34875513, year = {2021}, author = {Iasakov, TR and Kanapatskiy, TA and Toshchakov, SV and Korzhenkov, AA and Ulyanova, MO and Pimenov, NV}, title = {The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation.}, journal = {Marine environmental research}, volume = {173}, number = {}, pages = {105533}, doi = {10.1016/j.marenvres.2021.105533}, pmid = {34875513}, issn = {1879-0291}, abstract = {Pockmarks are important "pumps", which are believed to play a significant role in the global methane cycling and harboring a unique assemblage of very diverse prokaryotes. This study reports the results of massive sequencing of the 16S rRNA gene V4 hypervariable regions for the samples from thirteen pockmark horizons (the Baltic Sea) collected at depths from 0 to 280 cm below seafloor (cmbsf) and the rates of microbially mediated anaerobic oxidation of methane (AOM) and sulfate reduction (SR). Altogether, 76 bacterial and 12 archaeal phyla were identified, 23 of which were candidate divisions. Of the total obtained in the pockmark sequences, 84.3% of them were classified as Bacteria and 12.4% as Archaea; 3.3% of the sequences were assigned to unknown operational taxonomic units (OTUs). Members of the phyla Planctomycetota, Chloroflexota, Desulfobacterota, Caldatribacteriota, Acidobacteriota and Proteobacteria predominated across all horizons, comprising 58.5% of the total prokaryotic community. These phyla showed different types of patterns of relative abundance. Analysis of AOM-SR-mediated prokaryotes abundance and biogeochemical measurements revealed that ANME-2a-2b subcluster was predominant in sulfate-rich upper horizons (including sulfate-methane transition zone (SMTZ)) and together with sulfate-reducing bacterial group SEEP-SRB1 had a primary role in AOM coupled to SR. At deeper sulfate-depleted horizons ANME-2a-2b shifted to ANME-1a and ANME-1b which alone mediated AOM or switch to methanogenic metabolism. Shifting of the ANME subclusters depending on depth reflect a tendency for niche separation in these groups. It was shown that the abundance of Caldatribacteriota and organohalide-respiring Dehalococcoidia (Chloroflexota) exhibited a strong correlation with AOM rates. This is the first detailed study of depth profiles of prokaryotic diversity, patterns of relative abundance, and ANME niche separation in the Baltic Sea pockmark microbiomes sheds light on assembly of prokaryotes in a pockmark.}, }
@article {pmid34875269, year = {2021}, author = {Kim, H and Kim, M and Kim, S and Lee, YM and Shin, SC}, title = {Characterization of antimicrobial resistance genes and virulence factor genes in an Arctic permafrost region revealed by metagenomics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {118634}, doi = {10.1016/j.envpol.2021.118634}, pmid = {34875269}, issn = {1873-6424}, abstract = {Antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) constitute a serious threat to public health, and climate change has been predicted to affect the increase in bacterial pathogens harboring ARGs and VFGs. However, studies on bacterial pathogens and their ARGs and VFGs in permafrost region have received limited attention. In this study, a metagenomic approach was applied to a comprehensive survey to detect potential ARGs, VFGs, and pathogenic antibiotic resistant bacteria (PARB) carrying both ARGs and VFGs in the active layer and permafrost. Overall, 70 unique ARGs against 18 antimicrobial drug classes and 599 VFGs classified as 38 virulence factors were detected in the Arctic permafrost region. Eight genes with mobile genetic elements (MGEs) carrying ARGs were identified; most MGEs were classified as phages. In the metagenome-assembled genomes, the presence of 15 PARB was confirmed. The soil profile showed that the transcripts per million (TPM) values of ARGs and VFGs in the sub-soil horizon were significantly lower than those in the top soil horizon. Based on the TPM value of each gene, major ARGs, VFGs, and these genes in PARB from the Arctic permafrost region were identified and their distribution was confirmed. The major host bacteria for ARGs and VFGs and PARB were identified. A comparison of the percentage identity distribution of ARGs and VFGs to reference databases indicated that ARGs and VFGs in the Arctic soils differ from previously identified genes. Our results may help understand the characteristics and distribution of ARGs, VFGs, and these genes in PARB in the Arctic permafrost region. This findings suggest that the Arctic permafrost region may serve as potential reservoirs for ARGs, VFGs, and PARB. These genes could pose a new threat to human health if they are released by permafrost thawing owing to global warming and propagate to other regions.}, }
@article {pmid34875060, year = {2021}, author = {St James, AR and Richardson, RE}, title = {Stimulation of Dissimilatory Sulfate Reduction in Response to Sulfate in Microcosm Incubations from Two Contrasting Temperate Peatlands near Ithaca, NY, USA.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnab153}, pmid = {34875060}, issn = {1574-6968}, abstract = {Peatlands are responsible for over half of wetland methane emissions, yet major uncertainties remain regarding carbon flow, especially when increased availability of electron acceptors stimulate competing physiologies. We used microcosm incubations to study the effects of sulfate on microorganisms in two temperate peatlands, one bog and one fen. Three different electron donor treatments were used (13C-acetate, 13C-formate, and a mixture of 12C short-chain fatty acids) to elucidate the responses of sulfate-reducing bacteria (SRB) and methanogens to sulfate stimulation. Methane production was measured and metagenomic sequencing was performed, with only the heavy DNA fraction sequenced from treatments receiving 13C electron donors. Our data demonstrate stimulation of dissimilatory sulfate reduction in both sites, with contrasting community responses. In McLean Bog (MB), hydrogenotrophic Deltaproteobacteria and acetotrophic Peptococcaceae lineages of SRB were stimulated, as were lineages with unclassified dissimilatory sulfite reductases. In Michigan Hollow Fen (MHF), there was little stimulation of Peptococcaceae populations, and a small stimulation of Deltaproteobacteria SRB populations only in the presence of formate as electron donor. Sulfate stimulated an increase in relative abundance of reads for both oxidative and reductive sulfite reductases, suggesting stimulation of an internal sulfur cycle. Together, these data indicate a stimulation of SRB activity in response to sulfate in both sites, with a stronger growth response in MB than MHF. This study provides valuable insights into microbial community responses to sulfate in temperate peatlands and is an important first step to understanding how SRB and methanogens compete to regulate carbon flow in these systems.}, }
@article {pmid34874776, year = {2021}, author = {Grim, SL and Voorhies, AA and Biddanda, BA and Jain, S and Nold, SC and Green, R and Dick, GJ}, title = {Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O2 Cyanobacterial Mat Community.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0104221}, doi = {10.1128/mSystems.01042-21}, pmid = {34874776}, issn = {2379-5077}, abstract = {Cyanobacterial mats profoundly influenced Earth's biological and geochemical evolution and still play important ecological roles in the modern world. However, the biogeochemical functioning of cyanobacterial mats under persistent low-O2 conditions, which dominated their evolutionary history, is not well understood. To investigate how different metabolic and biogeochemical functions are partitioned among community members, we conducted metagenomics and metatranscriptomics on cyanobacterial mats in the low-O2, sulfidic Middle Island sinkhole (MIS) in Lake Huron. Metagenomic assembly and binning yielded 144 draft metagenome assembled genomes, including 61 of medium quality or better, and the dominant cyanobacteria and numerous Proteobacteria involved in sulfur cycling. Strains of a Phormidium autumnale-like cyanobacterium dominated the metagenome and metatranscriptome. Transcripts for the photosynthetic reaction core genes psaA and psbA were abundant in both day and night. Multiple types of psbA genes were expressed from each cyanobacterium, and the dominant psbA transcripts were from an atypical microaerobic type of D1 protein from Phormidium. Further, cyanobacterial transcripts for photosystem I genes were more abundant than those for photosystem II, and two types of Phormidium sulfide quinone reductase were recovered, consistent with anoxygenic photosynthesis via photosystem I in the presence of sulfide. Transcripts indicate active sulfur oxidation and reduction within the cyanobacterial mat, predominately by Gammaproteobacteria and Deltaproteobacteria, respectively. Overall, these genomic and transcriptomic results link specific microbial groups to metabolic processes that underpin primary production and biogeochemical cycling in a low-O2 cyanobacterial mat and suggest mechanisms for tightly coupled cycling of oxygen and sulfur compounds in the mat ecosystem. IMPORTANCE Cyanobacterial mats are dense communities of microorganisms that contain photosynthetic cyanobacteria along with a host of other bacterial species that play important yet still poorly understood roles in this ecosystem. Although such cyanobacterial mats were critical agents of Earth's biological and chemical evolution through geological time, little is known about how they function under the low-oxygen conditions that characterized most of their natural history. Here, we performed sequencing of the DNA and RNA of modern cyanobacterial mat communities under low-oxygen and sulfur-rich conditions from the Middle Island sinkhole in Lake Huron. The results reveal the organisms and metabolic pathways that are responsible for both oxygen-producing and non-oxygen-producing photosynthesis as well as interconversions of sulfur that likely shape how much O2 is produced in such ecosystems. These findings indicate tight metabolic reactions between community members that help to explain the limited the amount of O2 produced in cyanobacterial mat ecosystems.}, }
@article {pmid34874773, year = {2021}, author = {Maatouk, M and Ibrahim, A and Rolain, JM and Merhej, V and Bittar, F}, title = {Small and Equipped: the Rich Repertoire of Antibiotic Resistance Genes in Candidate Phyla Radiation Genomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0089821}, doi = {10.1128/mSystems.00898-21}, pmid = {34874773}, issn = {2379-5077}, abstract = {Microbes belonging to Candidate Phyla Radiation (CPR) have joined the tree of life as a new branch, thanks to the intensive application of metagenomics and sequencing technologies. CPR have been eventually identified by 16S rRNA analysis, and they represent more than 26% of microbial diversity. Despite their ultrasmall size, reduced genome, and metabolic pathways which mainly depend on exosymbiotic or exoparasitic relationships with the bacterial host, CPR microbes were found to be abundant in almost all environments. They can be considered survivors in highly competitive circumstances within microbial communities. However, their defense mechanisms and phenotypic characteristic remain poorly explored. Here, we conducted a thorough in silico analysis on 4,062 CPR genomes to search for antibiotic resistance (AR)-like enzymes using BLASTp and functional domain predictions against an exhaustive consensus AR database and conserved domain database (CDD), respectively. Our findings showed that a rich reservoir of divergent AR-like genes (n = 30,545 hits, mean = 7.5 hits/genome [0 to 41]) were distributed across the 13 CPR superphyla. These AR-like genes encode 89 different enzymes that are associated with 14 different chemical classes of antimicrobials. Most hits found (93.6%) were linked to glycopeptide, beta-lactam, macrolide-lincosamide-streptogramin (MLS), tetracycline, and aminoglycoside resistance. Moreover, two AR profiles were discerned for the Microgenomates group and "Candidatus Parcubacteria," which were distinct between them and differed from all other CPR superphyla. CPR cells seem to be active players during microbial competitive interactions; they are well equipped for microbial combat in different habitats, which ensures their natural survival and continued existence. IMPORTANCE To our knowledge, this study is one of the few studies that characterize the defense systems in the CPR group and describes the first repertoire of antibiotic resistance (AR) genes. The use of a BLAST approach with lenient criteria followed by a careful examination of the functional domains has yielded a variety of enzymes that mainly give three different mechanisms of action of resistance. Our genome analysis showed the existence of a rich reservoir of CPR resistome, which is associated with different antibiotic families. Moreover, this analysis revealed the hidden face of the reduced-genome CPR, particularly their weaponry with AR genes. These data suggest that CPR are competitive players in the microbial war, and they can be distinguished by specific AR profiles.}, }
@article {pmid34874772, year = {2021}, author = {Hilts, AS and Hunjan, MS and Hug, LA}, title = {Adapting Macroecology to Microbiology: Using Occupancy Modeling To Assess Functional Profiles across Metagenomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0079021}, doi = {10.1128/mSystems.00790-21}, pmid = {34874772}, issn = {2379-5077}, abstract = {Metagenomic sequencing provides information on the metabolic capacities and taxonomic affiliations for members of a microbial community. When assessing metabolic functions in a community, missing genes in pathways can occur in two ways; the genes may legitimately be missing from the community whose DNA was sequenced, or the genes were missed during shotgun sequencing or failed to assemble, and thus the metabolic capacity of interest is wrongly absent from the sequence data. Here, we borrow and adapt occupancy modeling from macroecology to provide mathematical context to metabolic predictions from metagenomes. We review the five assumptions underlying occupancy modeling through the lens of microbial community sequence data. Using the methane cycle, we apply occupancy modeling to examine the presence and absence of methanogenesis and methanotrophy genes from nearly 10,000 metagenomes spanning global environments. We determine that methanogenesis and methanotrophy are positively correlated across environments, providing a predictive framework for assessing gene absences for these functions. We present this adaptation of macroecology's occupancy modeling to metagenomics as a tool to quantify the uncertainty in predictions of the presence/absence of traits in environmental microbiological surveys. We further initiate a call for stronger metadata standards to accompany metagenome deposition, to enable robust statistical approaches in the future. IMPORTANCE Metagenomics is maturing rapidly as a field but is hampered by a lack of available statistical tools. A primary area of uncertainty is around missing genes or functions from a metagenomic data set. Here, we borrow an established modeling approach from macroecology and adapt it to metagenomic data sets. Rather than multiple sampling trips to a specific area to detect a species of interest (e.g., identifying a cardinal in a forest), we leverage the enormous amount of information within a metagenome and use multiple gene markers for a function of interest (e.g., subunits of an enzyme complex). We applied our adapted occupancy modeling to a case study examining methane cycling capacity. Our models show methanogens and methanotrophs are both more likely to cooccur than be present in the absence of the other guild. The lack of consistent and complete metadata is a significant hurdle for increasing the statistical rigor of metagenomic analyses.}, }
@article {pmid34874700, year = {2021}, author = {Fitzpatrick, KJ and Rohlf, HJ and Sutherland, TD and Koo, KM and Beckett, S and Okelo, WO and Keyburn, AL and Morgan, BS and Drigo, B and Trau, M and Donner, E and Djordjevic, SP and De Barro, PJ}, title = {Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains.}, journal = {ACS sensors}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssensors.1c01973}, pmid = {34874700}, issn = {2379-3694}, abstract = {The spread of antimicrobial resistance (AMR) is a rapidly growing threat to humankind on both regional and global scales. As countries worldwide prepare to embrace a One Health approach to AMR management, which is one that recognizes the interconnectivity between human, animal, and environmental health, increasing attention is being paid to identifying and monitoring key contributing factors and critical control points. Presently, AMR sensing technologies have significantly progressed phenotypic antimicrobial susceptibility testing (AST) and genotypic antimicrobial resistance gene (ARG) detection in human healthcare. For effective AMR management, an evolution of innovative sensing technologies is needed for tackling the unique challenges of interconnected AMR across various and different health domains. This review comprehensively discusses the modern state-of-play for innovative commercial and emerging AMR sensing technologies, including sequencing, microfluidic, and miniaturized point-of-need platforms. With a unique view toward the future of One Health, we also provide our perspectives and outlook on the constantly changing landscape of AMR sensing technologies beyond the human health domain.}, }
@article {pmid34874614, year = {2021}, author = {Weissenböck, H and Ebinger, A and Gager, AM and Thaller, D and Höper, D and Lichtmannsperger, K and Weissenbacher-Lang, C and Matt, J and Beer, M}, title = {A novel enterovirus in lambs with poliomyelitis and brain stem encephalitis.}, journal = {Transboundary and emerging diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/tbed.14412}, pmid = {34874614}, issn = {1865-1682}, abstract = {An Austrian organic dairy sheep farm experienced cases of recumbency and sudden deaths in three to four week old lambs. Two animals were subjected to thorough clinical and pathological investigations. Pathohistological analysis identified severe nonsuppurative myelitis and mild nonsuppurative encephalitis. An RT-qPCR assay for the recently discovered ovine picornavirus causing comparable lesions scored negative. By next-generation sequencing-based metagenomics a nearly complete genome of a novel enterovirus could be detected and assembled. In situ hybridization using a specifically designed probe revealed robust signals in affected motoneurons of the spinal cord suggesting a causative role of the novel virus. This article is protected by copyright. All rights reserved.}, }
@article {pmid34873691, year = {2021}, author = {Liu, Y and Zhang, F}, title = {Comparison of whole goat milk and their major fractions in modulating gut microbiota.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.11708}, pmid = {34873691}, issn = {1097-0010}, abstract = {BACKGROUND: Goat milk has been an important part of human nutrition because of its high nutritional values and these nutritional values can be attributed to its richness in protein, lactose, fat and other bioactive components. This study compared the diversity and composition of gut microbiota in response to whole goat milk and its major fractions (milk fat, casein, milk whey, whey protein and whey supernatant). Goat milk, major fractions and sterile distilled water (control group) were intragastrically administered to mice, respectively, and gut microbiota were compared in these seven groups using metagenomic analysis.<br><br>RESULTS: We observed distinct patterns of gut microbiota from different diet groups. The sample distance heatmap showed that compared with other goat milk fractions, gut microbiota in casein group was more similar to that in whole goat milk group. The relative abundance of genus Lactobacillus was significantly increased after whole goat milk treatment; milk whey fraction increased the abundance of Blautia; milk fat and milk whey related fractions treatment promoted the population of Bacteroides. The network analysis showed that genera Lactobacillus and Lactococcus were negatively associated with Helicobacter and Acinetobacter, respectively.<br><br>CONCLUSION: Major fractions of goat milk could result in different composition of gut microbiota from whole goat milk. Intake certain goat milk fraction could rise the abundance of beneficial bacteria and inhibit the growth of some pathogenic bacteria. Our results could provide the basis for the research and development of goat milk-based functional foods. This article is protected by copyright. All rights reserved.}, }
@article {pmid34873295, year = {2021}, author = {Reji, L and Cardarelli, EL and Boye, K and Bargar, JR and Francis, CA}, title = {Diverse ecophysiological adaptations of subsurface Thaumarchaeota in floodplain sediments revealed through genome-resolved metagenomics.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {34873295}, issn = {1751-7370}, support = {DE-SC0019119//DOE | SC | Biological and Environmental Research (BER)/ ; DE- AC02-76SF00515//DOE | SC | Biological and Environmental Research (BER)/ ; }, abstract = {The terrestrial subsurface microbiome contains vastly underexplored phylogenetic diversity and metabolic novelty, with critical implications for global biogeochemical cycling. Among the key microbial inhabitants of subsurface soils and sediments are Thaumarchaeota, an archaeal phylum that encompasses ammonia-oxidizing archaea (AOA) as well as non-ammonia-oxidizing basal lineages. Thaumarchaeal ecology in terrestrial systems has been extensively characterized, particularly in the case of AOA. However, there is little knowledge on the diversity and ecophysiology of Thaumarchaeota in deeper soils, as most lineages, particularly basal groups, remain uncultivated and underexplored. Here we use genome-resolved metagenomics to examine the phylogenetic and metabolic diversity of Thaumarchaeota along a 234 cm depth profile of hydrologically variable riparian floodplain sediments in the Wind River Basin near Riverton, Wyoming. Phylogenomic analysis of the metagenome-assembled genomes (MAGs) indicates a shift in AOA population structure from the dominance of the terrestrial Nitrososphaerales lineage in the well-drained top ~100 cm of the profile to the typically marine Nitrosopumilales in deeper, moister, more energy-limited sediment layers. We also describe two deeply rooting non-AOA MAGs with numerous unexpected metabolic features, including the reductive acetyl-CoA (Wood-Ljungdahl) pathway, tetrathionate respiration, a form III RuBisCO, and the potential for extracellular electron transfer. These MAGs also harbor tungsten-containing aldehyde:ferredoxin oxidoreductase, group 4f [NiFe]-hydrogenases and a canonical heme catalase, typically not found in Thaumarchaeota. Our results suggest that hydrological variables, particularly proximity to the water table, impart a strong control on the ecophysiology of Thaumarchaeota in alluvial sediments.}, }
@article {pmid34873157, year = {2021}, author = {Liu, X and Tong, X and Zhu, J and Tian, L and Jie, Z and Zou, Y and Lin, X and Liang, H and Li, W and Ju, Y and Qin, Y and Zou, L and Lu, H and Zhu, S and Jin, X and Xu, X and Yang, H and Wang, J and Zong, Y and Liu, W and Hou, Y and Jia, H and Zhang, T}, title = {Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome.}, journal = {Cell discovery}, volume = {7}, number = {1}, pages = {117}, pmid = {34873157}, issn = {2056-5968}, abstract = {The oral microbiota contains billions of microbial cells, which could contribute to diseases in many body sites. Challenged by eating, drinking, and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than 1915 individuals, for both the tongue dorsum (n = 2017) and saliva (n = 1915). We identified five genetic loci associated with oral microbiota at study-wide significance (p < 3.16 × 10-11). Four of the five associations were well replicated in an independent cohort of 1439 individuals: rs1196764 at APPL2 with Prevotella jejuni, Oribacterium uSGB 3339 and Solobacterium uSGB 315; rs3775944 at the serum uric acid transporter SLC2A9 with Oribacterium uSGB 1215, Oribacterium uSGB 489 and Lachnoanaerobaculum umeaense; rs4911713 near OR11H1 with species F0422 uSGB 392; and rs36186689 at LOC105371703 with Eggerthia. Further analyses confirmed 84% (386/455 for tongue dorsum) and 85% (391/466 for saliva) of host genome-microbiome associations including six genome-wide significant associations mutually validated between the two niches. As many of the oral microbiome-associated genetic variants lie near miRNA genes, we tentatively validated the potential of host miRNAs to modulate the growth of specific oral bacteria. Human genetics accounted for at least 10% of oral microbiome compositions between individuals. Machine learning models showed that polygenetic risk scores dominated over oral microbiome in predicting risk of dental diseases such as dental calculus and gingival bleeding. These findings indicate that human genetic differences are one explanation for a stable or recurrent oral microbiome in each individual.}, }
@article {pmid34873092, year = {2022}, author = {Yanavich, C and Perazzo, H and Li, F and Tobin, N and Lee, D and Zabih, S and Morata, M and Almeida, C and Veloso, VG and Grinsztejn, B and Aldrovandi, GM}, title = {A pilot study of microbial signatures of liver disease in those with HIV mono-infection in Rio de Janeiro, Brazil.}, journal = {AIDS (London, England)}, volume = {36}, number = {1}, pages = {49-58}, doi = {10.1097/QAD.0000000000003084}, pmid = {34873092}, issn = {1473-5571}, abstract = {OBJECTIVE: The rectal microbiome was examined to assess the relationship between the microbiome and liver disease in HIV-infection.<br><br>DESIGN: Eighty-two HIV-1 mono-infected individuals from the PROSPEC-HIV-study (NCT02542020) were grouped into three liver health categories based on results of controlled attenuation parameter (CAP) and liver stiffness measurement (LSM) of transient elastography: normal (n = 30), steatosis (n = 30), or fibrosis (n = 22).<br><br>METHODS: Liver steatosis and fibrosis were defined by CAP at least 248 dB/m and LSM at least 8.0 kPa, respectively. 16S rRNA gene and whole genome shotgun metagenomic sequencing were performed on rectal swabs. Bacterial differences were assessed using zero-inflated negative binomial regression and random forests modeling; taxonomic drivers of functional shifts were identified using FishTaco.<br><br>RESULTS: Liver health status explained four percentage of the overall variation (r2 = 0.04, P = 0.003) in bacterial composition. Participants with steatosis had depletions of Akkermansia muciniphila and Bacteroides dorei and enrichment of Prevotella copri, Finegoldia magna, and Ruminococcus bromii. Participants with fibrosis had depletions of Bacteroides stercoris and Parabacteroides distasonis and enrichment of Sneathia sanguinegens. In steatosis, functional analysis revealed increases in primary and secondary bile acid synthesis encoded by increased Eubacterium rectale, F. magna, and Faecalibacterium prausnitzii and decreased A. muciniphila, Bacteroides fragilis and B. dorei. Decreased folate biosynthesis was driven by similar changes in microbial composition.<br><br>CONCLUSION: HIV mono-infection with steatosis or fibrosis had distinct microbial profiles. Some taxa are similar to those associated with non-alcoholic fatty liver disease in HIV-negative populations. Further studies are needed to define the role of the gut microbiota in the pathogenesis of liver disease in HIV-infected persons.}, }
@article {pmid34873061, year = {2021}, author = {Yang, P and Zheng, W and Ning, K and Zhang, Y}, title = {Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {49}, pages = {}, doi = {10.1073/pnas.2110828118}, pmid = {34873061}, issn = {1091-6490}, abstract = {Information derived from metagenome sequences through deep-learning techniques has significantly improved the accuracy of template free protein structure modeling. However, most of the deep learning-based modeling studies are based on blind sequence database searches and suffer from low efficiency in computational resource utilization and model construction, especially when the sequence library becomes prohibitively large. We proposed a MetaSource model built on 4.25 billion microbiome sequences from four major biomes (Gut, Lake, Soil, and Fermentor) to decode the inherent linkage of microbial niches with protein homologous families. Large-scale protein family folding experiments on 8,700 unknown Pfam families showed that a microbiome targeted approach with multiple sequence alignment constructed from individual MetaSource biomes requires more than threefold less computer memory and CPU (central processing unit) time but generates contact-map and three-dimensional structure models with a significantly higher accuracy, compared with that using combined metagenome datasets. These results demonstrate an avenue to bridge the gap between the rapidly increasing metagenome databases and the limited computing resources for efficient genome-wide database mining, which provides a useful bluebook to guide future microbiome sequence database and modeling development for high-accuracy protein structure and function prediction.}, }
@article {pmid34873013, year = {2021}, author = {Mao, J and Wang, D and Long, J and Yang, X and Lin, J and Song, Y and Xie, F and Xun, Z and Wang, Y and Wang, Y and Li, Y and Sun, H and Xue, J and Song, Y and Zuo, B and Zhang, J and Bian, J and Zhang, T and Yang, X and Zhang, L and Sang, X and Zhao, H}, title = {Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers.}, journal = {Journal for immunotherapy of cancer}, volume = {9}, number = {12}, pages = {}, doi = {10.1136/jitc-2021-003334}, pmid = {34873013}, issn = {2051-1426}, abstract = {BACKGROUND: The gut microbiome is associated with the response to immunotherapy for different cancers. However, the impact of the gut microbiome on hepatobiliary cancers receiving immunotherapy remains unknown. This study aims to investigate the relationship between the gut microbiome and the clinical response to anti-programmed cell death protein 1 (PD-1) immunotherapy in patients with advanced hepatobiliary cancers.<br><br>METHODS: Patients with unresectable hepatocellular carcinoma or advanced biliary tract cancers who have progressed from first-line chemotherapy (gemcitabine plus cisplatin) were enrolled. Fresh stool samples were collected before and during anti-PD-1 treatment and analyzed with metagenomic sequencing. Significantly differentially enriched taxa and prognosis associated taxa were identified. The Kyoto Encyclopedia of Genes and Genomes database and MetaCyc database were further applied to annotate the differentially enriched taxa to explore the potential mechanism of the gut microbiome influencing cancer immunotherapy.<br><br>RESULTS: In total, 65 patients with advanced hepatobiliary cancers receiving anti-PD-1 treatment were included in this study. Seventy-four taxa were significantly enriched in the clinical benefit response (CBR) group and 40 taxa were significantly enriched in the non-clinical benefit (NCB) group. Among these taxa, patients with higher abundance of Lachnospiraceae bacterium-GAM79 and Alistipes sp Marseille-P5997, which were significantly enriched in the CBR group, achieved longer progression-free survival (PFS) and overall survival (OS) than patients with lower abundance. Higher abundance of Ruminococcus calidus and Erysipelotichaceae bacterium-GAM147 enriched in the CBR group was also observed in patients with better PFS. In contrast, worse PFS and OS were found in patients with higher abundance of Veillonellaceae, which was significantly enriched in the NCB group. Functional annotation indicated that the taxa enriched in the CBR group were associated with energy metabolism while the taxa enriched in the NCB group were associated with amino acid metabolism, which may modulate the clinical response to immunotherapy in hepatobiliary cancers. In addition, immunotherapy-related adverse events were affected by the gut microbiome diversity and relative abundance.<br><br>CONCLUSIONS: We demonstrate that the gut microbiome is associated with the clinical response to anti-PD-1 immunotherapy in patients with hepatobiliary cancers. Taxonomic signatures enriched in responders are effective biomarkers to predict the clinical response and survival benefit of immunotherapy, which might provide a new therapeutic target to modulate the response to cancer immunotherapy.}, }
@article {pmid34872580, year = {2021}, author = {Zeng, J and Wang, Y and Zhang, J and Yang, S and Zhang, W}, title = {Multiple novel filamentous phages detected in the cloacal swab samples of birds using viral metagenomics approach.}, journal = {Virology journal}, volume = {18}, number = {1}, pages = {240}, pmid = {34872580}, issn = {1743-422X}, support = {BE2017693//Jiangsu Provincial Key Research and Development Program/ ; 81741062//National Natural Science Foundation of China/ ; 12JDG085//Professional Research Foundation for Advanced Talents of Jiangsu University/ ; 13JDG087//Research Foundation for Advanced Talents of Ludong University/ ; }, abstract = {Members of the family Inoviridae (inoviruses) are characterized by their unique filamentous morphology and infection cycle. The viral genome of inovirus is able to integrate into the host genome and continuously releases virions without lysing the host, establishing chronic infection. A large number of inoviruses have been obtained from microbial genomes and metagenomes recently, but putative novel inoviruses remaining to be identified. Here, using viral metagenomics, we identified four novel inoviruses from cloacal swab samples of wild and breeding birds. The circular genome of those four inoviruses are 6732 to 7709 nt in length with 51.4% to 56.5% GC content and encodes 9 to 13 open reading frames, respectively. The zonula occludens toxin gene implicated in the virulence of pathogenic host bacteria were identified in all four inoviruses and shared the highest amino acid sequences identity (< 37.3%) to other reference strains belonging to different genera of the family Inoviridae and among themselves. Phylogenetic analysis indicated that all the four inoviruses were genetically far away from other strains belonging to the family Inoviridae and formed an independent clade. According to the genetic distance-based criteria, all the four inoviruses identified in the present study respectively belong to four novel putative genera in the family Inoviridae.}, }
@article {pmid34872176, year = {2022}, author = {Chen, X and Hu, X and Lu, Q and Yang, Y and Linghu, S and Zhang, X}, title = {Study on the differences in sludge toxicity and microbial community structure caused by catechol, resorcinol and hydroquinone with metagenomic analysis.}, journal = {Journal of environmental management}, volume = {302}, number = {Pt A}, pages = {114027}, doi = {10.1016/j.jenvman.2021.114027}, pmid = {34872176}, issn = {1095-8630}, abstract = {The aerobic biodegradation rate, organic toxicity and microbial community structure of activated sludge acclimated by catechol, resorcinol and hydroquinone were investigated, to study the relationship between microbial structure and sludge organic toxicity caused by phenolic compounds. At the stable operation stage, the degradation rates of the dihydroxy benzenes in a single sequencing batch reactor (SBR) cycle were followed the order: resorcinol (89.71%) > hydroquinone (85.64%) > catechol (59.62%). Sludge toxicity bioassay indicated that the toxicity of sludge was catechol (45.63%) > hydroquinone (40.28%) > resorcinol (38.15%). The accumulation of secondary metabolites such as 5-10 kDa tryptophan and tyrosine protein substances caused the differential sludge toxicity. Microbial metagenomic analysis showed that the toxicity of sludge was significantly related to the microbial community structure. Thauera, Azoarcus, Pseudomonas and other Proteobacteria formed in the sludge during acclimation. Catechol group had the least dominant bacteria and loop ring opening enzyme genes (catA, dmpB, dxnF, hapD) numbers. Therefore, the degradation of catechol was the most difficult than resorcinol and hydroquinone, resulting the highest sludge toxicity.}, }
@article {pmid34871697, year = {2021}, author = {Tong, C and Xiao, D and Xie, L and Yang, J and Zhao, R and Hao, J and Huo, Z and Zeng, Z and Xiong, W}, title = {Swine manure facilitates the spread of antibiotic resistome including tigecycline-resistant tet(X) variants to farm workers and receiving environment.}, journal = {The Science of the total environment}, volume = {808}, number = {}, pages = {152157}, doi = {10.1016/j.scitotenv.2021.152157}, pmid = {34871697}, issn = {1879-1026}, abstract = {The prevalence of antibiotic resistance genes (ARGs) in livestock and poultry manure is a severe threat to human health. However, the comprehensive characterization of antibiotic resistance in swine, workers, and the receiving environment is still lacking in the actual breeding environment. Hence, the ARG profile and the potential bacterial hosts producing among swine manure (including sows, piglets, finishing pigs, and nursery pigs), worker feces, and the receiving environment (including sediment and vegetable soil) were comprehensively analyzed based on the metagenomic method. The results showed that swine manure exhibited the high levels of richness and diversity of ARGs. Inactivating tetracycline resistance genes such as tet(X), tet(X1), and tet(X10) were prevalent on swine farms. Workers and the environment were the primary recipients of ARGs, and shared ARGs accounted for at least 90% of their ARG abundances. Network analysis revealed that Escherichia, Acinetobacter, and Erysipelothrix were the most dominant genera co-occurring with specific shared ARGs. The abundance of coexisting ARGs in swine at different developmental stages accounted for 76.4% to 90.8% of the shared ARGs in swine, workers, and environmental samples. The Mantel test revealed that Firmicutes and Proteobacteria had a significant correlation with the ARG profiles. In addition, variation partitioning analysis (VPA) showed that the joint effects of mobile genetic elements (MGEs) and bacterial communities accounted for 24.7% of the resistome variation and played a significant role in the ARG profiles. These results improve our understanding of the transmission and persistence of ARGs in the actual breeding environment.}, }
@article {pmid34871608, year = {2021}, author = {Liu, Y and Wang, Q and Pan, Q and Zhou, X and Peng, Z and Jahng, D and Yang, B and Pan, X}, title = {Ventilation induced evolution pattern of archaea, fungi, bacteria and their potential roles during co-bioevaporation treatment of concentrated landfill leachate and food waste.}, journal = {Chemosphere}, volume = {289}, number = {}, pages = {133122}, doi = {10.1016/j.chemosphere.2021.133122}, pmid = {34871608}, issn = {1879-1298}, abstract = {To obtain a favorable aeration type in co-bioevaporation treatment of concentrated landfill leachate and food waste, and to deeply understand the co-bioevaporation mechanisms, the temporal evolution differences of archaea, fungi and bacteria as well as the related microbial metabolism genes and functional enzymes under intermittent ventilation (IV) and continuous ventilation (CV) were investigated. Results through metagenomics analysis showed that the less sufficient oxygen and longer thermophilic phase in IV stimulated the vigorous growth of archaea, while CV was beneficial for fungal growth. Even genes of carbohydrates and lipids metabolism and ATP-associated enzymes (enzyme 2.7.13.3 and 3.6.4.12), as well as peptidoglycan biosynthesis enzyme (enzyme 3.4.16.4), were more abundant in CV, IV hold better DNA repair ability, higher microbial viability, and less dehydrogenase sensitivity to temperatures due to the critical contribution of Pseudomonas (3.1-45.9%). Furthermore, IV consumed a similar amount of heat for water evaporation with nearly half of the ventilation of CV and was a favorable aeration type in the practical application of co-bioevaporation.}, }
@article {pmid34871595, year = {2021}, author = {Liu, X and Tang, R and Li, H and Wang, L and Wan, C}, title = {The physiological and ecological properties of bacterial persisters discovered from municipal sewage sludge and the potential risk.}, journal = {Environmental research}, volume = {205}, number = {}, pages = {112481}, doi = {10.1016/j.envres.2021.112481}, pmid = {34871595}, issn = {1096-0953}, abstract = {Bacterial persisters are a special microbial population and are considered to be the bacterial reservoir of antibiotic-resistant bacteria. They can survive antibiotic treatment even in high concentrations of antibiotics and revive in the appropriate conditions. However, the characteristics of bacterial persisters in the municipal sewage sludge and their potential environmental risks have not yet been paid much attention to. In this study, bacterial persisters were discovered from the sludge of wastewater treatment plants in four different regions (Jilin, Lhasa, Shenzhen, and Yili), and the metagenomic analysis confirmed that bacterial persisters were ubiquitous in all four municipal sewage sludge and positively related to the protobacterium populations. At the taxonomic genus level, a total of 57 genera of bacterial persisters were shared by the four sewage sludge, and the genera with abundance exceeding 2% were Acinetobacter, Lysinibacillus, Aeromonas, Brevundimonas, Pseudomonas, and Alcaligenes, among which Acinetobacter accounted for 57.24%. Genus Lysinibacillus and Aeromonas were significant in Jilin and Lhasa, respectively. The persistence mechanism of bacterial persisters derived from sludge was also clarified, among which, Aeromonas, Brevundimonas, and Alcaligenes rely on the hipBA toxin-antitoxin system, while Acinetobacter enters the persistence state mainly through the stringent response system based on (p)ppGpp. Moreover, it was found that a typical bacterial persister originated from Acinetobacter, named T9-9, could tolerate a variety of antibiotics, such as 1000 μg/mL of kanamycin, 160 μg/mL of tetracycline, and 30 μg/mL of ciprofloxacin. Even if the ultraviolet intensity was 6-36 times the usual dosage of ultraviolet disinfection in wastewater treatment plants, it could not completely kill T9-9, but the killing efficiency by chlorine disinfection technology could reach 100%. This study pointed out an environmental risk of bacterial persisters that existed in sewage sludge that had been neglected and strongly recommended to improve the disinfection process in the wastewater treatment plant.}, }
@article {pmid34870848, year = {2021}, author = {Chen, J and Li, Y and Jing, H and Zhang, X and Xu, Z and Xu, J and Liu, H}, title = {Genomic and transcriptomic evidence for the diverse adaptations of subclusters 5.2 and 5.3 Synechococcus to mesoscale eddies.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.17903}, pmid = {34870848}, issn = {1469-8137}, abstract = {Mesoscale eddies are ubiquitous oceanographic features that influence the metabolism and community structure of Synechococcus. However, the metabolic adaptations of this genus to eddy-associated environmental changes have rarely been studied. We recovered two high-quality Synechococcus metagenome-assembled genomes (MAGs) from eddies in the South China Sea and compared their metabolic variations using metatranscriptomic samples obtained at the same time. The two MAGs (syn-bin1 and syn-bin2) are affiliated with marine Synechococcus subclusters 5.2 (S5.2) and 5.3 (S5.3), respectively. The former exhibited a higher abundance at the surface layer, whereas the latter was more abundant in deep euphotic layer. Further analysis indicated that syn-bin1 had a strong capability to utilize organic nutrients, which could help it to thrive in the nutrient-deprived surface water. In contrast, syn-bin2 had the genetic potential to perform chromatic acclimation, which could allow it to capture green or blue light at different depths. Additionally, transcriptomic analysis showed that syn-bin2 upregulated genes involved in the synthesis of C4 acids, photosystem II proteins, and HCO3 - transporters in deep euphotic layer, which might contribute to its predominance in low-light environment. Overall, this study extends our understanding of oceanic S5.2 and S5.3 Synechococcus by revealing their metabolic adaptations to mesoscale eddies.}, }
@article {pmid34870622, year = {2022}, author = {Redd, TK and Lalitha, P and Prajna, NV and Sikha, M and Gunasekaran, R and Hinterwirth, A and Chen, C and Zhong, L and Liu, Z and Lietman, TM and Keenan, JD and Doan, T and Seitzman, GD}, title = {Impact of Sample Collection Order on the Diagnostic Performance of Metagenomic Deep Sequencing for Infectious Keratitis.}, journal = {Cornea}, volume = {41}, number = {1}, pages = {39-44}, pmid = {34870622}, issn = {1536-4798}, support = {K08 EY026986/EY/NEI NIH HHS/United States ; P30 EY002162/EY/NEI NIH HHS/United States ; }, abstract = {PURPOSE: The purpose of this article was to evaluate the impact of sample collection order on the diagnostic yield of metagenomic deep sequencing (MDS) for determining the causative pathogen in infectious keratitis.<br><br>METHODS: We performed a cross-sectional diagnostic test evaluation among subjects with infectious keratitis at Aravind Eye Hospital in Madurai, India. All subjects underwent corneal scrapings of the affected eye to obtain potassium hydroxide smear, Gram stain, bacterial culture, and fungal culture, in this order. The order of MDS specimen collection relative to smear and culture samples was randomized and served as the primary predictor. Outcomes included the normalized copy number of pathogenic RNA detected by MDS, the proportion of MDS samples that were diagnostic, and the agreement of MDS results with cultures.<br><br>RESULTS: MDS samples from 46 subjects with corneal ulcers were evaluated. MDS was positive in 33 subjects (76%) and had 74% overall agreement with culture results. There was no association between order of MDS sample collection and normalized copy number of genetic material detected (P = 0.62) or the likelihood of MDS positivity (P = 0.46). However, the likelihood of agreement between MDS and cultures decreased when MDS corneal swabs were collected after other diagnostic corneal scrapings (P = 0.05).<br><br>CONCLUSIONS: The overall yield of MDS for detecting the cause of infectious keratitis was not affected by sample collection order. However, diagnostic agreement between MDS and cultures decreased when MDS samples were collected after other specimens. Additional investigation is warranted to determine whether this represents increased sensitivity of MDS compared with cultures or higher susceptibility to contaminants.}, }
@article {pmid34869767, year = {2021}, author = {Yu, X and Jiang, W and Huang, X and Lin, J and Ye, H and Liu, B}, title = {rRNA Analysis Based on Long-Read High-Throughput Sequencing Reveals a More Accurate Diagnostic for the Bacterial Infection of Ascites.}, journal = {BioMed research international}, volume = {2021}, number = {}, pages = {6287280}, pmid = {34869767}, issn = {2314-6141}, abstract = {Traditional pathogenic diagnosis presents defects such as a low positivity rate, inability to identify uncultured microorganisms, and time-consuming nature. Clinical metagenomics next-generation sequencing can be used to detect any pathogen, compensating for the shortcomings of traditional pathogenic diagnosis. We report third-generation long-read sequencing results and second-generation short-read sequencing results for ascitic fluid from a patient with liver ascites and compared the two types of sequencing results with the results of traditional clinical microbial culture. The distribution of pathogenic microbial species revealed by the two types of sequencing results was quite different, and the third-generation sequencing results were consistent with the results of traditional microbial culture, which can effectively guide subsequent treatment. Short reads, the lack of amplification, and enrichment to amplify signals from trace pathogens, and host background noise may be the reasons for the high error in the second-generation short-read sequencing results. Therefore, we propose that long-read-based rRNA analysis technology is superior to the short-read shotgun-based metagenomics method in the identification of pathogenic bacteria.}, }
@article {pmid34869737, year = {2021}, author = {Ning, S and Lu, X and Zhao, M and Wang, X and Yang, S and Shen, Q and Wang, H and Zhang, W}, title = {Virome in Fecal Samples From Wild Giant Pandas (Ailuropoda Melanoleuca).}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {767494}, pmid = {34869737}, issn = {2297-1769}, abstract = {The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals in the world; anthropogenic habitat loss and poaching still threaten the survival of wild pandas. Viral infection has become one of the potential threats to the health of these animals, but the available information related to these infections is still limited. In order to detect possible vertebrate viruses, the virome in the fecal samples of seven wild giant pandas from Qinling Mountains was investigated by using the method of viral metagenomics. From the fecal virome of wild giant pandas, we determined six nearly complete genomes belonging to the order Picornavirales, two of which may be qualified as a novel virus family or genus. In addition, four complete genomes belonging to the Genomoviridae family were also fully characterized. This virological investigation has increased our understanding of the gut viral community in giant pandas. Whether these viruses detected in fecal samples can really infect giant panda needs further research.}, }
@article {pmid34869453, year = {2021}, author = {Sun, L and Li, P and Pang, B and Wu, P and Wang, R}, title = {Gestational Psittacosis With Secondary Hemophagocytic Syndrome: A Case Report and Literature Review.}, journal = {Frontiers in medicine}, volume = {8}, number = {}, pages = {755669}, pmid = {34869453}, issn = {2296-858X}, abstract = {Gestational psittacosis and hemophagocytic syndrome (HPS) are rare clinical diseases. In this article, a case of gestational psittacosis concomitant with secondary HPS was reported. An analysis was performed on the clinical characteristics, signs, laboratory findings, progression, diagnosis, and treatment of a patient with gestational psittacosis concomitant with secondary HPS. Besides, the literature with respect to this disease was reviewed. This patient was definitively diagnosed through metagenomic next-generation sequencing techniques, bone marrow puncture and smear examination, and the determination of sCD25 level and natural killer (NK) cell activity. Anti-infectives such as doxycycline and etoposide combined with hormone chemotherapy achieved significant improvement in cough and expectoration, a return to normal temperature, and a significant improvement in oxygenation index. In addition, chest computed tomography revealed obvious absorption of lung lesions and a return of NK cell activity and sCD25 levels to normal ranges. Chlamydia psittaci pneumonia requires a clear determination of etiology, while HPS requires bone marrow puncture and smear examination, together with the determination of sCD25 level and NK cell activity in the blood. The findings of this study suggest that metagenomic next-generation sequencing is an effective instrument in clearly identifying pathogens that cause lung infection. Clinicians should consider atypical pathogens of lung infection in patients with poor response to empirical anti-infectives, and strive to design an effective treatment strategy as per an accurate diagnosis based on the etiology. As for patients suffering from long-term high fever and poor temperature control after broad-spectrum antibiotic treatment, non-infectious fever should be taken into account. A rapid and clear diagnosis would significantly improve patient prognosis.}, }
@article {pmid34869420, year = {2021}, author = {Arunasri, K and Sai Prashanthi, G and Tyagi, M and Pappuru, RR and Shivaji, S}, title = {Intraocular Viral Communities Associated With Post-fever Retinitis.}, journal = {Frontiers in medicine}, volume = {8}, number = {}, pages = {724195}, pmid = {34869420}, issn = {2296-858X}, abstract = {The virome of ocular fluids is naive. The results of this study highlight the virome in the vitreous fluid of the eye of individuals without any ocular infection and compare it with the virome of the vitreous fluid of individuals with retinitis. A total of 1,016,037 viral reads were generated from 25 vitreous fluid samples comprising control and post-fever retinitis (PFR) samples. The top 10 viral families in the vitreous fluids comprised of Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae, Poxviridae, Iridoviridae, Podoviridae, Retroviridae, Baculoviridae, and Flaviviridae. Principal coordinate analysis and heat map analysis clearly discriminated the virome of the vitreous fluid of the controls from that of the PFR virome. The abundance of 10 viral genera increased significantly in the vitreous fluid virome of the post-fever retinitis group compared with the control group. Genus Lymphocryptovirus, comprising the human pathogen Epstein-Barr virus (EBV) that is also implicated in ocular infections was significantly abundant in eight out of the nine vitreous fluid viromes of post-fever retinitis group samples compared with the control viromes. Human viruses, such as Hepacivirus, Circovirus, and Kobuvirus, were also significantly increased in abundance in the vitreous fluid viromes of post-fever retinitis group samples compared with the control viromes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analysis and the network analysis depicted an increase in the immune response by the host in the post-fever retinitis group compared with the control group. All together, the results of the study indicate changes in the virome in the vitreous fluid of patients with the post-fever retinitis group compared to the control group.}, }
@article {pmid34869341, year = {2021}, author = {Qin, Q and Yan, S and Yang, Y and Chen, J and Yan, H and Li, T and Gao, X and Wang, Y and Li, A and Wang, S and Ding, S}, title = {The Relationship Between Osteoporosis and Intestinal Microbes in the Henan Province of China.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {752990}, pmid = {34869341}, issn = {2296-634X}, abstract = {Osteoporosis (OP) is a chronic disease in the elderly, and China is entering an aging demographic trend. In recent years, increasing evidence has demonstrated that probiotics can treat osteoporosis. This study aimed to explore the relevant mechanisms and to validate the beneficial effect on osteoporosis by high-throughput metagenome-wide gene sequencing in humans. In this study, compared with controls, several species had altered abundances, and specific functional pathways were found in the OP group. At the species level, the species that had increased in OP individuals were positively correlated to bone resorption markers and negatively correlated to 25-OH-D3 and bone formation markers, with Streptococcus sanguinis showing the strongest relevance, followed by Streptococcus gordonii, Actinomyces odontolyticus, and Olsenella unclassified. Additionally, Actinomyces graevenitzii, enriched in the OP group, was positively correlated to inflammation indicators that included white blood cell (WBC), neutrophil count (NEC), and the neutrophil-to-lymphocyte ratio (NLR) (p < 0.05). Conversely, the levels of Akkermansia muciniphila, Bacteroides eggerthii, Bacteroides fragilis, Bacteroides uniformis, and Butyricimonas synergistic were increased in the control group, which had a negative correlation with bone resorption markers and positive correlation with bone formation markers and 25-OH-D3. Additionally, Bacteroides fragilis had a negative correlation with inflammation indicators (WBC, NEC, and NLR) and the above pathways (p < 0.05). Functional prediction revealed that 106 metabolic pathways, enriched in the OP group, were significantly higher than in the control group (p < 0.05). In particular, pathways related to LPS biosynthesis, phytate degradation, lactate acid, and ethanol fermentation were more abundant in the OP group than in the control and were positively related to WBC and NEC. Taken together, several species with altered abundances and specific functional pathways were found in OP individuals. The role of phytases in OP provides novel epidemiological evidence to elucidate the underlying microbiota-relevant mechanisms in bone mineralization and should be explored further.}, }
@article {pmid34869308, year = {2021}, author = {Pratt, M and Forbes, JD and Knox, NC and Bernstein, CN and Van Domselaar, G}, title = {Microbiome-Mediated Immune Signaling in Inflammatory Bowel Disease and Colorectal Cancer: Support From Meta-omics Data.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {716604}, pmid = {34869308}, issn = {2296-634X}, abstract = {Chronic intestinal inflammation and microbial dysbiosis are hallmarks of colorectal cancer (CRC) and inflammatory bowel diseases (IBD), such as Crohn's disease and ulcerative colitis. However, the mechanistic relationship between gut dysbiosis and disease has not yet been fully characterized. Although the "trigger" of intestinal inflammation remains unknown, a wealth of evidence supports the role of the gut microbiome as a mutualistic pseudo-organ that significantly influences intestinal homeostasis and is capable of regulating host immunity. In recent years, culture-independent methods for assessing microbial communities as a whole (termed meta-omics) have grown beyond taxonomic identification and genome characterization (metagenomics) into new fields of research that collectively expand our knowledge of microbiomes. Metatranscriptomics, metaproteomics, and metabolomics are meta-omics techniques that aim to describe and quantify the functional activity of the gut microbiome. Uncovering microbial metabolic contributions in the context of IBD and CRC using these approaches provides insight into how the metabolic microenvironment of the GI tract shapes microbial community structure and how the microbiome, in turn, influences the surrounding ecosystem. Immunological studies in germ-free and wild-type mice have described several host-microbiome interactions that may play a role in autoinflammation. Chronic colitis is a precursor to CRC, and changes in the gut microbiome may be an important link triggering the neoplastic process in chronic colitis. In this review, we describe several microbiome-mediated mechanisms of host immune signaling, such as short-chain fatty acid (SCFA) and bile acid metabolism, inflammasome activation, and cytokine regulation in the context of IBD and CRC, and discuss th