@article {pmid36152674,
year = {2022},
author = {Corander, J and Hanage, WP and Pensar, J},
title = {Causal discovery for the microbiome.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2666-5247(22)00186-0},
pmid = {36152674},
issn = {2666-5247},
abstract = {Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases in humans, developing new therapies, and finding preventive measures. Many studies have found significant associations between the microbiome and various diseases; however, Koch's classical postulates remind us about the importance of causative reasoning when considering the relationship between microbes and a disease manifestation. Although causal discovery in observational microbiome data faces many challenges, methodological advances in causal structure learning have improved the potential of data-driven prediction of causal effects in large-scale biological systems. In this Personal View, we show the capability of existing methods for inferring causal effects from metagenomic data, and we highlight ways in which the introduction of causal structures that are more flexible than existing structures offers new opportunities for causal reasoning. Our observations suggest that microbiome research can further benefit from tools developed in the past 5 years in causal discovery and learn from their applications elsewhere.},
}

@article {pmid36152543,
year = {2022},
author = {Yang, G and Xu, H and Luo, Y and Hei, S and Song, G and Huang, X},
title = {Novel electro-assisted micro-aerobic cathode biological technology induces oxidative demethylation of N, N-dimethylformamide for efficient ammonification of refractory membrane-making wastewater.},
journal = {Journal of hazardous materials},
volume = {442},
number = {},
pages = {130001},
doi = {10.1016/j.jhazmat.2022.130001},
pmid = {36152543},
issn = {1873-3336},
abstract = {Recalcitrant and toxicological membrane-making wastewater displays negative impacts on environment, and this is difficult to treat efficiently using conventional hydrolytic acidification. In this study, a novel electro-assisted biological reactor with micro-aerobic cathode (EABR-MAC) was developed to improve the biodegradation and ammonification of N, N-dimethylformamide (DMF) in membrane-making wastewater, and the metabolic mechanism using metagenomic sequencing as comprehensively illustrated. The results showed that EABR-MAC significantly improved the ammonification of refractory organonitrogen and promoted DMF oxidative degradation by driving the electron transferred to the cathode. Additionally, the inhibition rates of oxygen uptake rate and nitrification in EABR-MAC were both lower under different cathode aeration frequency conditions. Microbial community analysis indicated that the functional fermentation bacteria and exoelectrogens, which were correlated with COD removal, ammonification, and detoxification, were significantly enriched upon electrostimulation, and the positive biological connections increased to form highly connected communities instead of competition. The functional genes revealed that EABR-MAC forcefully intervened with the metabolic pathway, so that DMF converted to formamide and ammonia by oxidative demethylation and formamide hydrolysis. The results of this study provide a promising strategy for efficient conversion of organonitrogen into ammonia nitrogen, and offer a new insight into the effects of electrostimulation on microbial metabolism.},
}

@article {pmid36152521,
year = {2022},
author = {Grose, C},
title = {Metagenomic sequencing of cerebrospinal fluid from children with meningitis.},
journal = {EBioMedicine},
volume = {84},
number = {},
pages = {104287},
doi = {10.1016/j.ebiom.2022.104287},
pmid = {36152521},
issn = {2352-3964},
}

@article {pmid36151459,
year = {2022},
author = {Yamamoto, M and Takaki, Y and Kashima, H and Tsuda, M and Tanizaki, A and Nakamura, R and Takai, K},
title = {In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {36151459},
issn = {1751-7370},
support = {24244091//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 26610188//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20K20347//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 24244091//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20K20347//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; AB271008//MEXT | National Institutes of Natural Sciences (NINS)/ ; },
abstract = {Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was observed for 12 days of deployment, with fluctuation in response to tidal cycles. A novel bacterium belonging to the genus Thiomicrorhabdus dominated the microbial community specifically enriched on the cathode. Metagenomic analysis provided the draft genome of the bacterium and the gene repertoire indicated that the bacterium has the potential for thio-autotrophic growth, which is a typical physiological feature of the members of the genus, while the bacterium had a unique gene cluster encoding multi-heme cytochrome c proteins responsible for extracellular electron transfer. Herein, we propose this bacterium as a new species, specifically enriched during electricity generation, as 'Candidatus Thiomicrorhabdus electrophagus'. This finding suggests the natural occurrence of electrosynthetic microbial populations using the geoelectricity in deep-sea hydrothermal environments.},
}

@article {pmid36151458,
year = {2022},
author = {Maciel-Guerra, A and Baker, M and Hu, Y and Wang, W and Zhang, X and Rong, J and Zhang, Y and Zhang, J and Kaler, J and Renney, D and Loose, M and Emes, RD and Liu, L and Chen, J and Peng, Z and Li, F and Dottorini, T},
title = {Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {36151458},
issn = {1751-7370},
support = {104986//Innovate UK/ ; 104986//Innovate UK/ ; 104986//Innovate UK/ ; 104986//Innovate UK/ ; 104986//Innovate UK/ ; 104986//Innovate UK/ ; 104986//Innovate UK/ ; 2018YFE0101500//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2018YFE0101500//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2018YFE0101500//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2018YFE0101500//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; },
abstract = {A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.},
}

@article {pmid36151114,
year = {2022},
author = {Dekkers, KF and Sayols-Baixeras, S and Baldanzi, G and Nowak, C and Hammar, U and Nguyen, D and Varotsis, G and Brunkwall, L and Nielsen, N and Eklund, AC and Bak Holm, J and Nielsen, HB and Ottosson, F and Lin, YT and Ahmad, S and Lind, L and Sundström, J and Engström, G and Smith, JG and Ärnlöv, J and Orho-Melander, M and Fall, T},
title = {An online atlas of human plasma metabolite signatures of gut microbiome composition.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {5370},
pmid = {36151114},
issn = {2041-1723},
support = {2019-01471//Vetenskapsrådet (Swedish Research Council)/ ; 20190505//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; ERC-2018-STG801965//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Human gut microbiota produce a variety of molecules, some of which enter the bloodstream and impact health. Conversely, dietary or pharmacological compounds may affect the microbiota before entering the circulation. Characterization of these interactions is an important step towards understanding the effects of the gut microbiota on health. In this cross-sectional study, we used deep metagenomic sequencing and ultra-high-performance liquid chromatography linked to mass spectrometry for a detailed characterization of the gut microbiota and plasma metabolome, respectively, of 8583 participants invited at age 50 to 64 from the population-based Swedish CArdioPulmonary bioImage Study. Here, we find that the gut microbiota explain up to 58% of the variance of individual plasma metabolites and we present 997 associations between alpha diversity and plasma metabolites and 546,819 associations between specific gut metagenomic species and plasma metabolites in an online atlas (https://gutsyatlas.serve.scilifelab.se/). We exemplify the potential of this resource by presenting novel associations between dietary factors and oral medication with the gut microbiome, and microbial species strongly associated with the uremic toxin p-cresol sulfate. This resource can be used as the basis for targeted studies of perturbation of specific metabolites and for identification of candidate plasma biomarkers of gut microbiota composition.},
}

@article {pmid36149894,
year = {2022},
author = {Zhang, L and Chen, L and Yu, XA and Duvallet, C and Isazadeh, S and Dai, C and Park, S and Frois-Moniz, K and Duarte, F and Ratti, C and Alm, EJ and Ling, F},
title = {MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes.},
journal = {PLoS computational biology},
volume = {18},
number = {9},
pages = {e1010472},
doi = {10.1371/journal.pcbi.1010472},
pmid = {36149894},
issn = {1553-7358},
abstract = {The metagenome embedded in urban sewage is an attractive new data source to understand urban ecology and assess human health status at scales beyond a single host. Analyzing the viral fraction of wastewater in the ongoing COVID-19 pandemic has shown the potential of wastewater as aggregated samples for early detection, prevalence monitoring, and variant identification of human diseases in large populations. However, using census-based population size instead of real-time population estimates can mislead the interpretation of data acquired from sewage, hindering assessment of representativeness, inference of prevalence, or comparisons of taxa across sites. Here, we show that taxon abundance and sub-species diversisty in gut-associated microbiomes are new feature space to utilize for human population estimation. Using a population-scale human gut microbiome sample of over 1,100 people, we found that taxon-abundance distributions of gut-associated multi-person microbiomes exhibited generalizable relationships with respect to human population size. Here and throughout this paper, the human population size is essentially the sample size from the wastewater sample. We present a new algorithm, MicrobiomeCensus, for estimating human population size from sewage samples. MicrobiomeCensus harnesses the inter-individual variability in human gut microbiomes and performs maximum likelihood estimation based on simultaneous deviation of multiple taxa's relative abundances from their population means. MicrobiomeCensus outperformed generic algorithms in data-driven simulation benchmarks and detected population size differences in field data. New theorems are provided to justify our approach. This research provides a mathematical framework for inferring population sizes in real time from sewage samples, paving the way for more accurate ecological and public health studies utilizing the sewage metagenome.},
}

@article {pmid36148930,
year = {2022},
author = {Pettke, A and Filén, F and Widgren, K and Jacks, A and Glans, H and Andreasson, S and Muradrasoli, S and Helgesson, S and Hauzenberger, E and Karlberg, ML and Walai, N and Bjerkner, A and Gourlé, H and Gredmark-Russ, S and Lindsjö, OK and Sondén, K and Asgeirsson, H},
title = {Ten-Week Follow-Up of Monkeypox Case-Patient, Sweden, 2022.},
journal = {Emerging infectious diseases},
volume = {28},
number = {10},
pages = {2074-2077},
doi = {10.3201/eid2810.221107},
pmid = {36148930},
issn = {1080-6059},
abstract = {A previously healthy male patient had detectable monkeypox virus DNA in saliva 76 days after laboratory confirmation of infection. A comprehensive characterization of viral kinetics and a detailed follow-up indicated a declining risk for transmission during the weeks after monkeypox symptoms appeared.},
}

@article {pmid36148364,
year = {2022},
author = {Yan, H and Li, Z and Xia, H and Li, Q and Bai, H},
title = {A case report on mixed pulmonary infection of Nocardia nova, Mycobacterium tuberculosis, and Aspergillus fumigatus based on metagenomic next-generation sequencing.},
journal = {Frontiers in public health},
volume = {10},
number = {},
pages = {927338},
doi = {10.3389/fpubh.2022.927338},
pmid = {36148364},
issn = {2296-2565},
abstract = {Background: Pulmonary infection is one of the common complications of long-term use of glucocorticoids. Severe infections not only increase the length of hospital stay and treatment costs but also cause progression or recurrence of the primary disease.

Case description: Herein, we reported a case of mixed pulmonary infection secondary to glucocorticoid use. Rare pathogens such as Nocardia nova, Mycobacterium tuberculosis, Aspergillus fumigatus, and cytomegalovirus were detected by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and lung puncture tissue. Combining the results of conventional pathogen detection and clinical symptoms, the patient was diagnosed with mixed pulmonary infection by multiple pathogens. After timely targeted medication, the patient was finally discharged with a good prognosis.

Conclusion: To our knowledge, this is the first case report on mixed pulmonary infection with pathogens including Nocardia nova, Mycobacterium tuberculosis, Aspergillus fumigatus, and human cytomegalovirus. As a new clinical diagnostic method, mNGS has great advantages in diagnosis of diseases such as mixed infections.},
}

@article {pmid36148301,
year = {2022},
author = {Tous, N and Marcos, S and Goodarzi Boroojeni, F and Pérez de Rozas, A and Zentek, J and Estonba, A and Sandvang, D and Gilbert, MTP and Esteve-Garcia, E and Finn, R and Alberdi, A and Tarradas, J},
title = {Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {884925},
doi = {10.3389/fphys.2022.884925},
pmid = {36148301},
issn = {1664-042X},
abstract = {Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doing so, improve the quality and sustainability of animal production. Here, we introduce the animal trials conducted with broiler chickens in the H2020 project HoloFood, and our strategy to implement hologenomic analyses in light of the initial results, which despite yielding negligible effects of tested feed additives, provide relevant information to understand how host genomic features, microbiota development dynamics and host-microbiota interactions shape animal welfare and performance. We report the most relevant results, propose hypotheses to explain the observed patterns, and outline how these questions will be addressed through the generation and analysis of animal-microbiota multi-omic data during the HoloFood project.},
}

@article {pmid36147838,
year = {2022},
author = {Liu, YH and Ma, YM and Tian, HO and Yang, B and Han, WX and Zhao, WH and Chai, HL and Zhang, ZS and Wang, LF and Chen, L and Xing, Y and Ding, YL and Zhao, L},
title = {First determination of DNA virus and some additional bacteria from Melophagus ovinus (sheep ked) in Tibet, China.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {988136},
doi = {10.3389/fmicb.2022.988136},
pmid = {36147838},
issn = {1664-302X},
abstract = {Melophagus ovinus (sheep ked) is one of the common ectoparasites in sheep. In addition to causing direct damage to the host through biting and sucking blood, sheep ked is a potential vector of helminths, protozoa, bacteria, and viruses. Sheep M. ovinus samples from three regions in Tibet were selected for DNA extraction. The 16S rDNA V3-V4 hypervariable region was amplified, after genomic DNA fragmentation, Illumina Hiseq libraries were constructed. The 16S rRNA sequencing and viral metagenomics sequencing were separately conducted on the Illumina Novaseq 6000 platform and molecular biology software and platforms were employed to analyze the sequencing data. Illumina PE250 sequencing results demonstrated that the dominant bacteria phylum in M. ovinus from Tibet, China was Proteobacteria, where 29 bacteria genera were annotated. The dominant bacterial genera were Bartonella, Wolbachia, and Arsenophonus; Bartonella chomelii, Wolbachia spp., and Arsenophonus spp. were the dominant bacterial species in M. ovinus from Tibet, China. We also detected Kluyvera intermedia, Corynebacterium maris DSM 45190, Planomicrobium okeanokoites, and Rhodococcus erythropolis, of which the relative abundance of Kluyvera intermedia was high. Illumina Hiseq sequencing results demonstrated that 4 virus orders were detected in M. ovinus from Tibet, China, and 3 samples were annotated into 29 families, 30 families, and 28 families of viruses, respectively. Virus families related to vertebrates and insects mainly included Mimiviridae, Marseilleviridae, Poxviridae, Ascoviridae, Iridoviridae, Baculoviridae, Hytrosaviridae, Nudiviridae, Polydnaviridae, Adomaviridae, Asfarviridae, Hepeviridae, Herpesviridae, and Retroviridae; at the species level, the relative abundance of Tupanvirus_soda_lake, Klosneuvirus_KNV1, and Indivirus_ILV1 was higher. African swine fever virus and many poxviruses from the family Poxviridae were detected, albeit their relative abundance was low. The dominant bacterial phylum of M. ovinus from Tibet, China was Proteobacteria, and the dominant bacterial genera were Bartonella, Wolbachia, and Arsenophonus, where 23 out of 29 annotated bacteria genera were first reported in M. ovinus. Kluyvera intermedia, Corynebacterium maris DSM 45190, Planomicrobium okeanokoites, and Rhodococcus erythropolis were detected for the first time. All DNA viruses detected in this study have been reported in M. ovinus for the first time.},
}

@article {pmid36147601,
year = {2022},
author = {Zhou, Z and Lv, H and Lv, J and Shi, Y and Huang, H and Chen, L and Shi, D},
title = {Alterations of gut microbiota in cirrhotic patients with spontaneous bacterial peritonitis: A distinctive diagnostic feature.},
journal = {Frontiers in cellular and infection microbiology},
volume = {12},
number = {},
pages = {999418},
doi = {10.3389/fcimb.2022.999418},
pmid = {36147601},
issn = {2235-2988},
abstract = {Background: Spontaneous bacterial peritonitis (SBP) is a severe infection in cirrhotic patients that requires early diagnosis to improve the long-term outcome. Alterations in the gut microbiota have been shown to correlate with the development and progression of liver cirrhosis. However, the relationship between SBP and gut microbiota remains unknown.

Methods: In this study, we applied 16S rRNA pyrosequencing of feces to ascertain possible links between the gut microbiota and SBP. We recruited 30 SBP patients, 30 decompensated cirrhotic patients without SBP (NSBP) and 30 healthy controls. Metagenomic functional prediction of bacterial taxa was achieved using PICRUSt.

Results: The composition of the gut microbiota in the SBP patients differed remarkably from that in the NSBP patients and healthy individuals. The microbial richness was significantly decreased, while the diversity was increased in the SBP patients. Thirty-four bacterial taxa containing 15 species, mainly pathogens such as Klebsiella pneumoniae, Serratia marcescens and Prevotella oris, were dominant in the SBP group, while 42 bacterial taxa containing 16 species, especially beneficial species such as Faecalibacterium prausnitzii, Methanobrevibacter smithii and Lactobacillus reuteri, were enriched in the NSBP group. Notably, we found that 18 gene functions of gut microbiota were different between SBP patients and NSBP patients, which were associated with energy metabolism and functional substance metabolism. Five optimal microbial markers were determined using a random forest model, and the combination of Lactobacillus reuteri, Rothia mucilaginosa, Serratia marcescens, Ruminococcus callidus and Neisseria mucosa achieved an area under the curve (AUC) value of 0.8383 to distinguish SBP from decompensated cirrhosis.

Conclusions: We described the obvious dysbiosis of gut microbiota in SBP patients and demonstrated the potential of microbial markers as noninvasive diagnostic tools for SBP at an early stage.},
}

@article {pmid36146871,
year = {2022},
author = {Sasivimolrattana, T and Chantratita, W and Sensorn, I and Chaiwongkot, A and Oranratanaphan, S and Bhattarakosol, P},
title = {Human Virome in Cervix Controlled by the Domination of Human Papillomavirus.},
journal = {Viruses},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/v14092066},
pmid = {36146871},
issn = {1999-4915},
support = {RA-MF-46/64//Ratchadaphiseksomphot Matching Fund/ ; CU_FRB640001_01_30_9//Thailand Science Research and Innovation Fund (TSRI)/ ; was received by T.S.//The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship/ ; was received by P.B. and T.S.//The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund)/ ; },
abstract = {Although other co-viral infections could also be considered influencing factors, cervical human papillomavirus (HPV) infection is the main cause of cervical cancer. Metagenomics have been employed in the NGS era to study the microbial community in each habitat. Thus, in this investigation, virome capture sequencing was used to examine the virome composition in the HPV-infected cervix. Based on the amount of HPV present in each sample, the results revealed that the cervical virome of HPV-infected individuals could be split into two categories: HPV-dominated (HD; ≥60%) and non-HPV-dominated (NHD; <60%). Cervical samples contained traces of several human viral species, including the molluscum contagiosum virus (MCV), human herpesvirus 4 (HHV4), torque teno virus (TTV), and influenza A virus. When compared to the HD group, the NHD group had a higher abundance of several viruses. Human viral diversity appears to be influenced by HPV dominance. This is the first proof that the diversity of human viruses in the cervix is impacted by HPV abundance. However, more research is required to determine whether human viral variety and the emergence of cancer are related.},
}

@article {pmid36146854,
year = {2022},
author = {Yang, S and Zhang, D and Ji, Z and Zhang, Y and Wang, Y and Chen, X and He, Y and Lu, X and Li, R and Guo, Y and Shen, Q and Ji, L and Wang, X and Li, Y and Zhang, W},
title = {Viral Metagenomics Reveals Diverse Viruses in Tissue Samples of Diseased Pigs.},
journal = {Viruses},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/v14092048},
pmid = {36146854},
issn = {1999-4915},
support = {2017YFC1200201//National Key Research and Development Programs of China/ ; BE2017693//Jiangsu Provincial Key Research and Development Projects/ ; 2020CPB-C11//Independent Project of Chengdu Research Base of Giant Panda Breeding/ ; },
abstract = {The swine industry plays an essential role in agricultural production in China. Diseases, especially viral diseases, affect the development of the pig industry and threaten human health. However, at present, the tissue virome of diseased pigs has rarely been studied. Using the unbiased viral metagenomic approach, we investigated the tissue virome in sick pigs (respiratory symptoms, reproductive disorders, high fever, diarrhea, weight loss, acute death and neurological symptoms) collected from farms of Anhui, Jiangsu and Sichuan Province, China. The eukaryotic viruses identified belonged to the families Anelloviridae, Arteriviridae, Astroviridae, Flaviviridae, Circoviridae and Parvoviridae; prokaryotic virus families including Siphoviridae, Myoviridae and Podoviridae occupied a large proportion in some samples. This study provides valuable information for understanding the tissue virome in sick pigs and for the monitoring, preventing, and treating of viral diseases in pigs.},
}

@article {pmid36146797,
year = {2022},
author = {Pérot, P and Bigot, T and Temmam, S and Regnault, B and Eloit, M},
title = {Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery.},
journal = {Viruses},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/v14091990},
pmid = {36146797},
issn = {1999-4915},
support = {Not applicable//Institut Pasteur/ ; },
abstract = {We present Microseek, a pipeline for virus identification and discovery based on RVDB-prot, a comprehensive, curated and regularly updated database of viral proteins. Microseek analyzes metagenomic Next Generation Sequencing (mNGS) raw data by performing quality steps, de novo assembly, and by scoring the Lowest Common Ancestor (LCA) from translated reads and contigs. Microseek runs on a local computer. The outcome of the pipeline is displayed through a user-friendly and dynamic graphical interface. Based on two representative mNGS datasets derived from human tissue and plasma specimens, we illustrate how Microseek works, and we report its performances. In silico spikes of known viral sequences, but also spikes of fake Neopneumovirus viral sequences generated with variable evolutionary distances from known members of the Pneumoviridae family, were used. Results were compared to Chan Zuckerberg ID (CZ ID), a reference cloud-based mNGS pipeline. We show that Microseek reliably identifies known viral sequences and performs well for the detection of distant pseudoviral sequences, especially in complex samples such as in human plasma, while minimizing non-relevant hits.},
}

@article {pmid36146789,
year = {2022},
author = {Busse, L and Tisza, M and DiRuggiero, J},
title = {Viruses Ubiquity and Diversity in Atacama Desert Endolithic Communities.},
journal = {Viruses},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/v14091983},
pmid = {36146789},
issn = {1999-4915},
support = {80NSSC19K0470/NASA/NASA/United States ; NNX15AP18G/NASA/NASA/United States ; },
abstract = {Viruses are key players in the environment, and recent metagenomic studies have revealed their diversity and genetic complexity. Despite progress in understanding the ecology of viruses in extreme environments, viruses' dynamics and functional roles in dryland ecosystems, which cover about 45% of the Earth's land surfaces, remain largely unexplored. This study characterizes virus sequences in the metagenomes of endolithic (within rock) microbial communities ubiquitously found in hyper-arid deserts. Taxonomic classification and network construction revealed the presence of novel and diverse viruses in communities inhabiting calcite, gypsum, and ignimbrite rocks. Viral genome maps show a high level of protein diversity within and across endolithic communities and the presence of virus-encoded auxiliary metabolic genes. Phage-host relationships were predicted by matching tRNA, CRISPR spacer, and protein sequences in the viral and microbial metagenomes. Primary producers and heterotrophic bacteria were found to be putative hosts to some viruses. Intriguingly, viral diversity was not correlated with microbial diversity across rock substrates.},
}

@article {pmid36146775,
year = {2022},
author = {Hesse, RD and Roach, M and Kerr, EN and Papudeshi, B and Lima, LFO and Goodman, AZ and Hoopes, L and Scott, M and Meyer, L and Huveneers, C and Dinsdale, EA},
title = {Phage Diving: An Exploration of the Carcharhinid Shark Epidermal Virome.},
journal = {Viruses},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/v14091969},
pmid = {36146775},
issn = {1999-4915},
support = {CO4145//S. Lo and B. Billings Global Shark Conservation Fund/ ; },
abstract = {The epidermal microbiome is a critical element of marine organismal immunity, but the epidermal virome of marine organisms remains largely unexplored. The epidermis of sharks represents a unique viromic ecosystem. Sharks secrete a thin layer of mucus which harbors a diverse microbiome, while their hydrodynamic dermal denticles simultaneously repel environmental microbes. Here, we sampled the virome from the epidermis of three shark species in the family Carcharhinidae: the genetically and morphologically similar Carcharhinus obscurus (n = 6) and Carcharhinus galapagensis (n = 10) and the outgroup Galeocerdo cuvier (n = 15). Virome taxonomy was characterized using shotgun metagenomics and compared with a suite of multivariate analyses. All three sharks retain species-specific but highly similar epidermal viromes dominated by uncharacterized bacteriophages which vary slightly in proportional abundance within and among shark species. Intraspecific variation was lower among C. galapagensis than among C. obscurus and G. cuvier. Using both the annotated and unannotated reads, we were able to determine that the Carcharhinus galapagensis viromes were more similar to that of G. cuvier than they were to that of C. obscurus, suggesting that behavioral niche may be a more prominent driver of virome than host phylogeny.},
}

@article {pmid36146740,
year = {2022},
author = {Souza, JVC and Santos, HO and Leite, AB and Giovanetti, M and Bezerra, RDS and Carvalho, E and Bernardino, JST and Viala, VL and Haddad, R and Ciccozzi, M and Alcantara, LCJ and Sampaio, SC and Covas, DT and Kashima, S and Elias, MC and Slavov, SN},
title = {Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification.},
journal = {Viruses},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/v14091933},
pmid = {36146740},
issn = {1999-4915},
support = {2017/23205-8//São Paulo Research Foundation/ ; },
abstract = {Viral metagenomics is increasingly being used for the identification of emerging and re-emerging viral pathogens in clinical samples with unknown etiology. The objective of this study was to shield light on the metavirome composition in clinical samples obtained from patients with clinical history compatible with an arboviral infection, but that presented inconclusive results when tested using RT-qPCR. The inconclusive amplification results might be an indication of the presence of an emerging arboviral agent that is inefficiently amplified by conventional PCR techniques. A total of eight serum samples with inconclusive amplification results for the routinely tested arboviruses-dengue (DENV), Zika (ZIKV), and Chikungunya (CHIKV) obtained during DENV and CHIKV outbreaks registered in the state of Alagoas, Northeast Brazil between July and August 2021-were submitted to metagenomic next-generation sequencing assay using NextSeq 2000 and bioinformatic pipeline for viral discovery. The performed bioinformatic analysis revealed the presence of two arboviruses: DENV type 2 (DENV-2) and CHIKV with a high genome coverage. Further, the metavirome of those samples revealed the presence of multiple commensal viruses apparently without clinical significance. The phylogenetic analysis demonstrated that the DENV-2 genome belonged to the Asian/American genotype and clustered with other Brazilian strains. The identified CHIKV genome was taxonomically assigned as ECSA genotype, which is circulating in Brazil. Together, our results reinforce the utility of metagenomics as a valuable tool for viral identification in samples with inconclusive arboviral amplification. Viral metagenomics is one of the most potent methods for the identification of emerging arboviruses.},
}

@article {pmid36146717,
year = {2022},
author = {Wiederkehr, MA and Qi, W and Schoenbaechler, K and Fraefel, C and Kubacki, J},
title = {Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland.},
journal = {Viruses},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/v14091911},
pmid = {36146717},
issn = {1999-4915},
support = {STWF-19-013//C.F. was supported by the Foundation for Research in Science and the Humanities at the University of Zurich/ ; },
abstract = {Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host.},
}

@article {pmid36146668,
year = {2022},
author = {Esnault, G and Earley, B and Cormican, P and Waters, SM and Lemon, K and Cosby, SL and Lagan, P and Barry, T and Reddington, K and McCabe, MS},
title = {Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1.},
journal = {Viruses},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/v14091859},
pmid = {36146668},
issn = {1999-4915},
support = {RMIS0345//Teagasc - The Irish Agriculture and Food Development Authority/ ; 16/RD/US-ROI/11//Department of Agriculture Food and the Marine/ ; },
abstract = {Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics sequencing on the portable, inexpensive Oxford Nanopore Technologies MinION sequencer and sequence analysis with its associated user-friendly point-and-click Epi2ME cloud-based pathogen identification software has the potential for point-of-care/same-day/sample-to-result metagenomic sequence diagnostics of known and unknown BRD pathogens to inform a rapid response and vaccine design. We assessed this potential using in vitro viral cell cultures and nasal swabs taken from calves that were experimentally challenged with a single known BRD-associated DNA virus, namely, bovine herpes virus 1. Extensive optimisation of the standard Oxford Nanopore library preparation protocols, particularly a reduction in the PCR bias of library amplification, was required before BoHV-1 could be identified as the main virus in the in vitro cell cultures and nasal swab samples within approximately 7 h from sample to result. In addition, we observed incorrect assignment of the bovine sequence to bacterial and viral taxa due to the presence of poor-quality bacterial and viral genome assemblies in the RefSeq database used by the EpiME Fastq WIMP pathogen identification software.},
}

@article {pmid36146660,
year = {2022},
author = {Howard-Jones, AR and Pham, D and Jeoffreys, N and Eden, JS and Hueston, L and Kesson, AM and Nagendra, V and Samarasekara, H and Newton, P and Chen, SC and O'Sullivan, MV and Maddocks, S and Dwyer, DE and Kok, J},
title = {Emerging Genotype IV Japanese Encephalitis Virus Outbreak in New South Wales, Australia.},
journal = {Viruses},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/v14091853},
pmid = {36146660},
issn = {1999-4915},
abstract = {The detection of a new and unexpected Japanese encephalitis virus (JEV) outbreak in March 2022 in Australia, where JEV is not endemic, demanded the rapid development of a robust diagnostic framework to facilitate the testing of suspected patients across the state of New South Wales (NSW). This nascent but comprehensive JEV diagnostic service encompassed serological, molecular and metagenomics testing within a centralised reference laboratory. Over the first three months of the outbreak (4 March 2022 to 31 May 2022), 1,061 prospective samples were received from 878 NSW residents for JEV testing. Twelve confirmed cases of Japanese encephalitis (JE) were identified, including ten cases diagnosed by serology alone, one case by metagenomic next generation sequencing and real-time polymerase chain reaction (RT-PCR) of brain tissue and serology, and one case by RT-PCR of cerebrospinal fluid, providing an incidence of JE over this period of 0.15/100,000 persons in NSW. As encephalitis manifests in <1% of cases of JEV infection, the population-wide prevalence of JEV infection is likely to be substantially higher. Close collaboration with referring laboratories and clinicians was pivotal to establishing successful JEV case ascertainment for this new outbreak. Sustained and coordinated animal, human and environmental surveillance within a OneHealth framework is critical to monitor the evolution of the current outbreak, understand its origins and optimise preparedness for future JEV and arbovirus outbreaks.},
}

@article {pmid36146653,
year = {2022},
author = {Yutin, N and Rayko, M and Antipov, D and Mutz, P and Wolf, YI and Krupovic, M and Koonin, EV},
title = {Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales.},
journal = {Viruses},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/v14091842},
pmid = {36146653},
issn = {1999-4915},
support = {Intramural funds/NH/NIH HHS/United States ; },
abstract = {Bacteriophages play key roles in the dynamics of the human microbiome. By far the most abundant components of the human gut virome are tailed bacteriophages of the realm Duplodnaviria, in particular, crAss-like phages. However, apart from duplodnaviruses, the gut virome has not been dissected in detail. Here we report a comprehensive census of a minor component of the gut virome, the tailless bacteriophages of the realm Varidnaviria. Tailless phages are primarily represented in the gut by prophages, that are mostly integrated in genomes of Alphaproteobacteria and Verrucomicrobia and belong to the order Vinavirales, which currently consists of the families Corticoviridae and Autolykiviridae. Phylogenetic analysis of the major capsid proteins (MCP) suggests that at least three new families should be established within Vinavirales to accommodate the diversity of prophages from the human gut virome. Previously, only the MCP and packaging ATPase genes were reported as conserved core genes of Vinavirales. Here we report an extended core set of 12 proteins, including MCP, packaging ATPase, and previously undetected lysis enzymes, that are shared by most of these viruses. We further demonstrate that replication system components are frequently replaced in the genomes of Vinavirales, suggestive of selective pressure for escape from yet unknown host defenses or avoidance of incompatibility with coinfecting related viruses. The results of this analysis show that, in a sharp contrast to marine viromes, varidnaviruses are a minor component of the human gut virome. Moreover, they are primarily represented by prophages, as indicated by the analysis of the flanking genes, suggesting that there are few, if any, lytic varidnavirus infections in the gut at any given time. These findings complement the existing knowledge of the human gut virome by exploring a group of viruses that has been virtually overlooked in previous work.},
}

@article {pmid36145435,
year = {2022},
author = {Balázs, B and Tóth, Z and Nagy, JB and Majoros, L and Tóth, Á and Kardos, G},
title = {Faecal Carriage of Carbapenem-Resistant Acinetobacter baumannii: Comparison to Clinical Isolates from the Same Period (2017-2019).},
journal = {Pathogens (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
doi = {10.3390/pathogens11091003},
pmid = {36145435},
issn = {2076-0817},
abstract = {Increasing prevalence of A. baumannii was found in the faecal samples of inpatients without infection caused by A. baumannii (0.15%; 55/7806). The aim of the study was to determine whether there is a relationship between the clinical strains and the increased faecal occurrence. Characteristics of faecal and clinical isolates were compared between 2017 and 2019, and the direction of causality was assessed by Granger causality tests. In the case of the antibiotic resistance, faecal carriage of carbapenem-resistant Acinetobacter baumannii (CRAb) was Granger-caused by prevalence of CRAb in inpatients (F = 15.84, p < 0.001), but inpatient prevalence was not Granger-caused by CRAb faecal carriage (F = 0.03, p = 0.855). Whole genomes of 16 faecal isolates were sequenced by Illumina MiSeq; cgMLST types were determined. In faecal isolates, the occurrence of carbapenem resistance was lower than among the clinical isolates from the same period; only blaOXA-72 harbouring ST636 and ST492 were detected, and the blaOXA-23 harbouring ST2 and ST49 strains previously dominant in clinical isolates were absent. Carriage of blaOXA-72 was linked to pMAL-1-like and pA105-2-like plasmids in ST636 and ST492 isolates, respectively, both in clinical and faecal isolates. The new ST636 and ST492 strains may colonise the gut microbiota of the patients, which thus may play a role as a reservoir.},
}

@article {pmid36145357,
year = {2022},
author = {Mokrousov, I and Slavchev, I and Solovieva, N and Dogonadze, M and Vyazovaya, A and Valcheva, V and Masharsky, A and Belopolskaya, O and Dimitrov, S and Zhuravlev, V and Portugal, I and Perdigão, J and Dobrikov, GM},
title = {Molecular Insight into Mycobacterium tuberculosis Resistance to Nitrofuranyl Amides Gained through Metagenomics-like Analysis of Spontaneous Mutants.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/ph15091136},
pmid = {36145357},
issn = {1424-8247},
support = {19-15-00028//Russian Science Foundation/ ; АААА-А21-121021600206-5//Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing/ ; KP-06-N39/7//Bulgarian Science Fund/ ; KP-06-N41/3//Bulgarian Science Fund/ ; UID/DTP/04138/2019//Fundação para a Ciência e Tecnologia/ ; CEECIND/00394/2017//Fundação para a Ciência e Tecnologia/ ; },
abstract = {We performed synthesis of new nitrofuranyl amides and investigated their anti-TB activity and primary genetic response of mycobacteria through whole-genome sequencing (WGS) of spontaneous resistant mutants. The in vitro activity was assessed on reference strain Mycobacterium tuberculosis H37Rv. The most active compound 11 was used for in vitro selection of spontaneous resistant mutants. The same mutations in six genes were detected in bacterial cultures grown under increased concentrations of 11 (2×, 4×, 8× MIC). The mutant positions were presented as mixed wild type and mutant alleles while increasing the concentration of the compound led to the semi-proportional and significant increase in mutant alleles. The identified genes belong to different categories and pathways. Some of them were previously reported as mediating drug resistance or drug tolerance, and counteracting oxidative and nitrosative stress, in particular: Rv0224c, fbiC, iniA, and Rv1592c. Gene-set interaction analysis revealed a certain weak interaction for gene pairs Rv1592-Rv1639c and Rv1592-Rv0224c. To conclude, this study experimentally demonstrated a multifaceted primary genetic response of M. tuberculosis to the action of nitrofurans. All three 11-treated subcultures independently presented the same six SNPs, which suggests their non-random occurrence and likely causative relationship between compound action and possible resistance mechanism.},
}

@article {pmid36145068,
year = {2022},
author = {Pang, L and Zhi, Q and Jian, W and Liu, Z and Lin, H},
title = {The Oral Microbiome Impacts the Link between Sugar Consumption and Caries: A Preliminary Study.},
journal = {Nutrients},
volume = {14},
number = {18},
pages = {},
doi = {10.3390/nu14183693},
pmid = {36145068},
issn = {2072-6643},
support = {81903345//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The excessive and frequent intake of refined sugar leads to caries. However, the relationship between the amount of sugar intake and the risk of caries is not always consistent. Oral microbial profile and function may impact the link between them. This study aims to identify the plaque microbiota characteristics of caries subjects with low (CL) and high (CH) sugar consumption, and of caries-free subjects with low (FL) and high sugar (FH) consumption.

METHODS: A total of 40 adolescents were enrolled in the study, and supragingival plaque samples were collected and subjected to metagenomic analyses. The caries status, sugar consumption, and oral-health behaviors of the subjects were recorded.

RESULTS: The results indicate that the CL group showed a higher abundance of several cariogenic microorganisms Lactobacillus, A. gerencseriae, A. dentails, S. mutans, C. albicans, S. wiggsiae and P. acidifaciens. C. gingivalis, and P. gingivalis, which were enriched in the FH group. In terms of gene function, the phosphotransferase sugar uptake system, phosphotransferase system, and several two-component responses-regulator pairs were enriched in the CL group.

CONCLUSION: Overall, our data suggest the existence of an increased cariogenic microbial community and sugar catabolism potential in the CL group, and a healthy microbial community in the FH group, which had self-stabilizing functional potential.},
}

@article {pmid36144468,
year = {2022},
author = {Syromyatnikov, M and Nesterova, E and Gladkikh, M and Smirnova, Y and Gryaznova, M and Popov, V},
title = {Characteristics of the Gut Bacterial Composition in People of Different Nationalities and Religions.},
journal = {Microorganisms},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/microorganisms10091866},
pmid = {36144468},
issn = {2076-2607},
support = {project FZGW-2020-0001, unique number of the register of State tasks 075001X39782002//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {High-throughput sequencing has made it possible to extensively study the human gut microbiota. The links between the human gut microbiome and ethnicity, religion, and race remain rather poorly understood. In this review, data on the relationship between gut microbiota composition and the nationality of people and their religion were generalized. The unique gut microbiome of a healthy European (including Slavic nationality) is characterized by the dominance of the phyla Firmicutes, Bacteroidota, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. Among the African population, the typical members of the microbiota are Bacteroides and Prevotella. The gut microbiome of Asians is very diverse and rich in members of the genera Prevotella, Bacteroides Lactobacillus, Faecalibacterium, Ruminococcus, Subdoligranulum, Coprococcus, Collinsella, Megasphaera, Bifidobacterium, and Phascolarctobacterium. Among Buddhists and Muslims, the Prevotella enterotype is characteristic of the gut microbiome, while other representatives of religions, including Christians, have the Bacteroides enterotype. Most likely, the gut microbiota of people of different nationalities and religions are influenced by food preferences. The review also considers the influences of pathologies such as obesity, Crohn's disease, cancer, diabetes, etc., on the bacterial composition of the guts of people of different nationalities.},
}

@article {pmid36144417,
year = {2022},
author = {Esposito, AM and Esposito, MM and Ptashnik, A},
title = {Phylogenetic Diversity of Animal Oral and Gastrointestinal Viromes Useful in Surveillance of Zoonoses.},
journal = {Microorganisms},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/microorganisms10091815},
pmid = {36144417},
issn = {2076-2607},
abstract = {Great emphasis has been placed on bacterial microbiomes in human and animal systems. In recent years, advances in metagenomics have allowed for the detection and characterization of more and more native viral particles also residing in these organisms. The digestive tracts of animals and humans-from the oral cavity, to the gut, to fecal excretions-have become one such area of interest. Next-generation sequencing and bioinformatic analyses have uncovered vast phylogenetic virome diversity in companion animals, such as dogs and cats, as well as farm animals and wildlife such as bats. Zoonotic and arthropod-borne illnesses remain major causes of worldwide outbreaks, as demonstrated by the devastating COVID-19 pandemic. This highlights the increasing need to identify and study animal viromes to prevent such disastrous cross-species transmission outbreaks in the coming years. Novel viruses have been uncovered in the viromes of multiple organisms, including birds, bats, cats, and dogs. Although the exact consequences for public health have not yet become clear, many analyses have revealed viromes dominated by RNA viruses, which can be the most problematic to human health, as these genomes are known for their high mutation rates and immune system evasion capabilities. Furthermore, in the wake of worldwide disruption from the COVID-19 pandemic, it is evident that proper surveillance of viral biodiversity is crucial. For instance, gut viral metagenomic analysis in dogs has shown close relationships between the highly abundant canine coronavirus and human coronavirus strains 229E and NL63. Future studies and vigilance could potentially save many lives.},
}

@article {pmid36144397,
year = {2022},
author = {Goel, A and Ncho, CM and Jeong, CM and Gupta, V and Jung, JY and Ha, SY and Yang, JK and Choi, YH},
title = {Effects of Dietary Supplementation of Solubles from Shredded, Steam-Exploded Pine Particles on the Performance and Cecum Microbiota of Acute Heat-Stressed Broilers.},
journal = {Microorganisms},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/microorganisms10091795},
pmid = {36144397},
issn = {2076-2607},
support = {2020193C10-2022-BA01//Korea Forest Service/ ; 2019H1D3A1A01071142//National Research Foundation of Korea/ ; },
abstract = {Heat stress (HS) negatively influences livestock productivity, but it can be, at least in part, mitigated by nutritional interventions. One such intervention is to use byproducts from various sources that are likely to be included in the consumer chain. Thus, the present study investigated the effects of dietary supplementation of solubles from shredded, steam-exploded pine particles (SSPPs) on the performance and cecum microbiota in broilers subjected to acute HS. One-week-old Ross 308 broilers (n = 108) were fed 0%, 0.1%, or 0.4% SSPP in their diets. On the 37th day, forty birds were allocated to one of four groups; namely, a group fed a control diet without SSPPs at thermoneutral temperature (NT) (0% NT) and acute heat-stressed birds with 0% (0% HS), 0.1% (0.1% HS), and 0.4% (0.4% HS) SSPP-supplemented diets. The NT was maintained at 21.0 °C, while the HS room was increased to 31 °C. The final BW, percent difference in body weight (PDBW), and feed intake (FI) were lower in HS birds, but PDBW was reversely associated with dietary SSPP. Similarly, HS birds had a higher rectal temperature (RT) and ΔT in comparison to birds kept at NT. The FI of SSPP-supplemented birds was not significant, indicating lower HS effects. Plasma triglyceride was decreased in HS birds but not affected in 0.1% HS birds in comparison to 0% NT birds. OTUs and Chao1 were increased by 0.1% HS compared to 0% NT. Unweighted Unifrac distances for 0.1% HS were different from 0% NT and 0.4% HS. The favorable bacterial phylum (Tenericutes) and genera (Faecalibacterium and Anaerofustis) were increased, while the pathogenic genus (Enterococcus) was decreased, in SSPP-supplemented birds. In sum, production performances are negatively affected under acute HS. Dietary supplementation of SSPPs is beneficial for improving community richness indices and unweighted Unifrac distances, and it enhanced the advantageous bacterial phyla and reduced virulent genera and triglyceride hydrolysis in acute HS broilers. Our results indicate that dietary SSPPs modulates the microbial profile of the cecum while resulting in relatively less weight loss and lower rectal temperature compared to control.},
}

@article {pmid36144349,
year = {2022},
author = {Gontijo, JB and Paula, FS and Venturini, AM and Mandro, JA and Bodelier, PLE and Tsai, SM},
title = {Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments.},
journal = {Microorganisms},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/microorganisms10091747},
pmid = {36144349},
issn = {2076-2607},
support = {2014/50320-4, 2017/26138-0, 2018/14974-0, 2019/25924-7, and 2019/25931-3//São Paulo Research Foundation/ ; },
abstract = {Although floodplains are recognized as important sources of methane (CH4) in the Amazon basin, little is known about the role of methanotrophs in mitigating CH4 emissions in these ecosystems. Our previous data reported the genus Methylocystis as one of the most abundant methanotrophs in these floodplain sediments. However, information on the functional potential and life strategies of these organisms living under seasonal flooding is still missing. Here, we described the first metagenome-assembled genome (MAG) of a Methylocystis sp. recovered from Amazonian floodplains sediments, and we explored its functional potential and ecological traits through phylogenomic, functional annotation, and pan-genomic approaches. Both phylogenomics and pan-genomics identified the closest placement of the bin.170_fp as Methylocystis parvus. As expected for Type II methanotrophs, the Core cluster from the pan-genome comprised genes for CH4 oxidation and formaldehyde assimilation through the serine pathway. Furthermore, the complete set of genes related to nitrogen fixation is also present in the Core. Interestingly, the MAG singleton cluster revealed the presence of unique genes related to nitrogen metabolism and cell motility. The study sheds light on the genomic characteristics of a dominant, but as yet unexplored methanotroph from the Amazonian floodplains. By exploring the genomic potential related to resource utilization and motility capability, we expanded our knowledge on the niche breadth of these dominant methanotrophs in the Amazonian floodplains.},
}

@article {pmid36144342,
year = {2022},
author = {Yang, Z and Yao, Y and Sun, M and Li, G and Zhu, J},
title = {Metagenomics Reveal Microbial Effects of Lotus Root-Fish Co-Culture on Nitrogen Cycling in Aquaculture Pond Sediments.},
journal = {Microorganisms},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/microorganisms10091740},
pmid = {36144342},
issn = {2076-2607},
support = {U20A2010//National Natural Science Foundation of China/ ; 2019YFD0900302//National Key Research and Development Program of China/ ; },
abstract = {Feed input leads to a large amount of nitrogen-containing sediment accumulating in the substrate in the pond culture process, threatening the safety of aquaculture production. Planting lotus roots (Nelumbo nucifera Gaertn.) in ponds can accelerate the removal of bottom nitrogen, while the role of nitrogen cycle-related microorganisms in the removal is still unclear. In this study, eight yellow catfish (Pelteobagrus fulvidraco) culture ponds with the same basic situation were divided into fishponds with planted lotus roots and ponds with only fish farming. Sediment samples were taken from the fishponds with planted lotus roots and the ponds with only fish farming before and after fish farming, marked as FPB, FPA, FOB, and FOA, respectively, and subjected to physicochemical and metagenomic sequencing analyses. The results show that the contents of NH4+, NO2-, TN, TP, and OM were significantly lower (p < 0.05) in FPA than in FOA. The abundance of metabolic pathways for inorganic nitrogen transformation and ammonia assimilation increased considerably after culture compared to the sediments before culture. A total of eight ammonia production pathways and two ammonia utilization pathways were annotated in the sediments of the experimental ponds, with a very high abundance of ammonia assimilation. Acinetobacter and Pseudomonas (34.67%, 18.02%) were the dominant bacteria in the pond sediments before culture, which changed to Thiobacillus (12.16%) after culture. The FPA had significantly higher relative abundances of Thiobacillus denitrificans and Sulfuricella denitrificans, and the FOA had significantly a higher abundance of Microcystis aeruginosa compared to other samples. The massive growth of Microcystis aeruginosa provided two new inorganic nitrogen metabolic pathways and one organic nitrogen metabolic pathway for FOA. The relative abundances of these three microorganisms were negatively correlated with NH4+ content (p < 0.01) and significantly positively correlated with AP, OM content, and pH value. Compared with ponds with only fish farming, lotus root-fish co-culture can significantly reduce the nitrogen content in sediment, increase the abundance of denitrifying bacteria, and inhibit algae growth. Still, it has little effect on the abundance of nitrogen cycle-related enzymes and genes. In summary, it is shown that, although lotus roots promote the growth of denitrifying microorganisms in the sediment, nitrogen removal relies mainly on nutrient uptake by lotus roots.},
}

@article {pmid36144222,
year = {2022},
author = {Miglani, R and Parveen, N and Kumar, A and Ansari, MA and Khanna, S and Rawat, G and Panda, AK and Bisht, SS and Upadhyay, J and Ansari, MN},
title = {Degradation of Xenobiotic Pollutants: An Environmentally Sustainable Approach.},
journal = {Metabolites},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/metabo12090818},
pmid = {36144222},
issn = {2218-1989},
abstract = {The ability of microorganisms to detoxify xenobiotic compounds allows them to thrive in a toxic environment using carbon, phosphorus, sulfur, and nitrogen from the available sources. Biotransformation is the most effective and useful metabolic process to degrade xenobiotic compounds. Microorganisms have an exceptional ability due to particular genes, enzymes, and degradative mechanisms. Microorganisms such as bacteria and fungi have unique properties that enable them to partially or completely metabolize the xenobiotic substances in various ecosystems.There are many cutting-edge approaches available to understand the molecular mechanism of degradative processes and pathways to decontaminate or change the core structure of xenobiotics in nature. These methods examine microorganisms, their metabolic machinery, novel proteins, and catabolic genes. This article addresses recent advances and current trends to characterize the catabolic genes, enzymes and the techniques involved in combating the threat of xenobiotic compounds using an eco-friendly approach.},
}

@article {pmid36144194,
year = {2022},
author = {Li-Gao, R and Grubbs, K and Bertoni, AG and Hoffman, KL and Petrosino, JF and Ramesh, G and Wu, M and Rotter, JI and Chen, YI and Evans, AM and Robinson, RJ and Sommerville, L and Mook-Kanamori, D and Goodarzi, MO and Michelotti, GA and Sheridan, PA},
title = {The Roles of Gut Microbiome and Plasma Metabolites in the Associations between ABO Blood Groups and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES).},
journal = {Metabolites},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/metabo12090787},
pmid = {36144194},
issn = {2218-1989},
support = {R01DK109588/NH/NIH HHS/United States ; UL1TR001881/TR/NCATS NIH HHS/United States ; DK063491//National Institute of Diabetes and Digestive and Kidney Disease Diabetes Research Center/ ; R01HL105756//National Heart Lung and Blood Institute/ ; },
abstract = {Non-O blood groups are associated with decreased insulin sensitivity and risk of type 2 diabetes. A recent study pinpointed the associations between ABO blood groups and gut microbiome, which may serve as potential mediators for the observed increased disease risks. We aimed to characterize associations between ABO haplotypes and insulin-related traits as well as potential mediating pathways. We assessed insulin homeostasis in African Americans (AAs; n = 109) and non-Hispanic whites (n = 210) from the Microbiome and Insulin Longitudinal Evaluation Study. The ABO haplotype was determined by six SNPs located in the ABO gene. Based on prior knowledge, we included 21 gut bacteria and 13 plasma metabolites for mediation analysis. In the white study cohort (60 ± 9 years, 42% male), compared to the O1 haplotype, A1 was associated with a higher Matsuda insulin sensitivity index, while a lower relative abundance of Bacteroides massiliensis and lactate levels. Lactate was a likely mediator of this association but not Bacteroides massiliensis. In the AAs group (57 ± 8 years, 33% male), we found no association between any haplotype and insulin-related traits. In conclusion, the A1 haplotype may promote healthy insulin sensitivity in non-Hispanic whites and lactate likely play a role in this process but not selected gut bacteria.},
}

@article {pmid36144180,
year = {2022},
author = {Wu, C and Fei, J and Xu, Q and Tao, Y and Zhou, Z and Wang, Y and Wu, J and Gu, HF},
title = {Interaction between Plasma Metabolomics and Intestinal Microbiome in db/db Mouse, an Animal Model for Study of Type 2 Diabetes and Diabetic Kidney Disease.},
journal = {Metabolites},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/metabo12090775},
pmid = {36144180},
issn = {2218-1989},
support = {CPU20190228HFG//Cooperation Research Grant/ ; CPU20180815HFG//China Pharmaceutical University/ ; },
abstract = {Evidence has demonstrated that either metabolites or intestinal microbiota are involved in the pathogenesis of type 2 diabetes (T2D) and diabetic kidney disease (DKD). To explore the interaction between plasma metabolomics and intestinal microbiome in the progress of T2D-DKD, in the current study, we analyzed metabolomics in the plasma of db/db mice with liquid chromatography-mass spectrometry and also examined intestinal prokaryotes and entire gut microbiome dysbiosis at the genus level with both 16S rDNA and metagenomic sequencing techniques. We found that Negativibacillus and Rikenella were upregulated, while Akkermansia, Candidatus, Erysipelatoclostridium and Ileibacterium were downregulated in the colon of db/db mice compared with non-diabetic controls. In parallel, a total of 91 metabolites were upregulated, while 23 were downregulated in the plasma of db/db mice. The top five upregulated metabolites included D-arabinose 5-phosphate, estrone 3-sulfate, L-theanine, 3'-aenylic acid and adenosine 5'-monophosphate, and the five most significantly downregulated metabolites were aurohyocholic acid sodium salt, calcium phosphorylcholine chloride, tauro-alpha-muricholic acid sodium salt, galactinol and phosphocholine. These plasma metabolites were interacted with intestinal microbiomes, which are mainly involved in the pathways related to the biosynthesis of unsaturated fatty acids, fatty acid elongation, steroid biosynthesis, and D-arginine and D-ornithine metabolism. In the differential metabolites, N-acetyl-L-ornithine, ornithine and L-kyn could be metabolized by the correspondingly differential ontology genes in the intestinal metagenome. The current study thereby provides evidence for a gut-metabolism-kidney axis in the metabolism of db/db mice, in which the gut microbiome and circulating metabolomics interact, and suggests that information from this axis may contribute to our understanding of T2D and DKD pathogenesis.},
}

@article {pmid36143456,
year = {2022},
author = {Olunoiki, E and Rehner, J and Bischoff, M and Koshel, E and Vogt, T and Reichrath, J and Becker, SL},
title = {Characteristics of the Skin Microbiome in Selected Dermatological Conditions: A Narrative Review.},
journal = {Life (Basel, Switzerland)},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/life12091420},
pmid = {36143456},
issn = {2075-1729},
abstract = {The skin is the largest and outermost organ of the human body. The microbial diversity of the skin can be influenced by several variable factors such as physiological state, lifestyle, and geographical locations. Recent years have seen increased interest in research aiming at an improved understanding of the relationship between the human microbiota and several diseases. Albeit understudied, interesting correlations between the skin microbiota and several dermatological conditions have been observed. Studies have shown that a decrease or increase in the abundance of certain microbial communities can be implicated in several dermatological pathologies. This narrative review (i) examines the role of the skin microbiota in the maintenance of skin homeostasis and health, (ii) provides examples on how some common skin diseases (acne inversa, candidiasis, psoriasis) are associated with the dysbiosis of microbial communities, and (iii) describes how recent research approaches used in skin microbiome studies may lead to improved, more sensitive diagnostics and individual therapeutics in the foreseeable future.},
}

@article {pmid36143382,
year = {2022},
author = {Tausch, SH and Loka, TP and Schulze, JM and Andrusch, A and Klenner, J and Dabrowski, PW and Lindner, MS and Nitsche, A and Renard, BY},
title = {PathoLive-Real-Time Pathogen Identification from Metagenomic Illumina Datasets.},
journal = {Life (Basel, Switzerland)},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/life12091345},
pmid = {36143382},
issn = {2075-1729},
support = {2515NIK043//Federal Ministry of Health/ ; Live-DREAM//Federal Ministry of Education and Research/ ; },
abstract = {Over the past years, NGS has become a crucial workhorse for open-view pathogen diagnostics. Yet, long turnaround times result from using massively parallel high-throughput technologies as the analysis can only be performed after sequencing has finished. The interpretation of results can further be challenged by contaminations, clinically irrelevant sequences, and the sheer amount and complexity of the data. We implemented PathoLive, a real-time diagnostics pipeline for the detection of pathogens from clinical samples hours before sequencing has finished. Based on real-time alignment with HiLive2, mappings are scored with respect to common contaminations, low-entropy areas, and sequences of widespread, non-pathogenic organisms. The results are visualized using an interactive taxonomic tree that provides an easily interpretable overview of the relevance of hits. For a human plasma sample that was spiked in vitro with six pathogenic viruses, all agents were clearly detected after only 40 of 200 sequencing cycles. For a real-world sample from Sudan, the results correctly indicated the presence of Crimean-Congo hemorrhagic fever virus. In a second real-world dataset from the 2019 SARS-CoV-2 outbreak in Wuhan, we found the presence of a SARS coronavirus as the most relevant hit without the novel virus reference genome being included in the database. For all samples, clinically irrelevant hits were correctly de-emphasized. Our approach is valuable to obtain fast and accurate NGS-based pathogen identifications and correctly prioritize and visualize them based on their clinical significance: PathoLive is open source and available on GitLab and BioConda.},
}

@article {pmid36143265,
year = {2022},
author = {Reider, S and Watschinger, C and Längle, J and Pachmann, U and Przysiecki, N and Pfister, A and Zollner, A and Tilg, H and Plattner, S and Moschen, AR},
title = {Short- and Long-Term Effects of a Prebiotic Intervention with Polyphenols Extracted from European Black Elderberry-Sustained Expansion of Akkermansia spp.},
journal = {Journal of personalized medicine},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/jpm12091479},
pmid = {36143265},
issn = {2075-4426},
support = {not applicable//Christian Doppler Research Association/ ; not applicable//IPRONA AG/SPA/ ; },
abstract = {(1) Background: The intestinal microbiome has emerged as a central factor in human physiology and its alteration has been associated with disease. Therefore, great hopes are placed in microbiota-modulating strategies. Among various approaches, prebiotics, substrates with selective metabolization conferring a health benefit to the host, are promising candidates. Herein, we studied the prebiotic properties of a purified extract from European black elderberries, with a high and standardized content of polyphenols and anthocyanins. (2) Methods: The ELDERGUT trial represents a 9-week longitudinal intervention study divided into 3 distinct phases, namely a baseline, an intervention and a washout period, three weeks each. The intervention consisted of capsules containing 300 mg elderberry extract taken twice a day. Patient-reported outcomes and biosamples were collected weekly. Microbiome composition was assessed using 16S amplicon metagenomics. (3) Results: The supplementation was well tolerated. Microbiome trajectories were highly individualized with a profound shift in diversity indices immediately upon initiation and after termination of the compound. This was accompanied by corresponding changes in species abundance over time. Of particular interest, the relative abundance of Akkermansia spp. continued to increase in a subset of participants even beyond the supplementation period. Associations with participant metadata were detected.},
}

@article {pmid36142786,
year = {2022},
author = {Mayorga, L and Serrano-Gómez, G and Xie, Z and Borruel, N and Manichanh, C},
title = {Intercontinental Gut Microbiome Variances in IBD.},
journal = {International journal of molecular sciences},
volume = {23},
number = {18},
pages = {},
doi = {10.3390/ijms231810868},
pmid = {36142786},
issn = {1422-0067},
support = {PI20/00130//Instituto de Salud Carlos III/ ; 812969/MCCC_/Marie Curie/United Kingdom ; PI17/00614//Instituto de Salud Carlos III/ ; },
abstract = {The development of biomarkers for inflammatory bowel disease (IBD) diagnosis would be relevant in a generalized context. However, intercontinental investigation on these microbial biomarkers remains scarce. We examined taxonomic microbiome variations in IBD using published DNA shotgun metagenomic data. For this purpose, we used sequenced data from our previous Spanish Crohn's disease (CD) and ulcerative colitis (UC) cohort, downloaded sequence data from a Chinese CD cohort, and downloaded taxonomic and functional profiling tables from a USA CD and UC cohort. At the global level, geographical location and disease phenotype were the main explanatory covariates of microbiome variations. In healthy controls (HC) and UC, geography turned out to be the most important factor, while disease intestinal location was the most important one in CD. Disease severity correlated with lower alpha-diversity in UC but not in CD. Across geography, alpha-diversity was significantly different independently of health status, except for CD. Despite recruitment from different countries and with different disease severity scores, CD patients may harbor a very similar microbial taxonomic profile. Our study pointed out that geographic location, disease activity status, and other environmental factors are important contributing factors in microbiota changes in IBD. We therefore strongly recommend taking these factors into consideration for future IBD studies to obtain globally valid and reproducible biomarkers.},
}

@article {pmid36142744,
year = {2022},
author = {Zhang, T and Huang, S and Qiu, J and Wu, X and Yuan, H and Park, S},
title = {Beneficial Effect of Gastrodia elata Blume and Poria cocos Wolf Administration on Acute UVB Irradiation by Alleviating Inflammation through Promoting the Gut-Skin Axis.},
journal = {International journal of molecular sciences},
volume = {23},
number = {18},
pages = {},
doi = {10.3390/ijms231810833},
pmid = {36142744},
issn = {1422-0067},
support = {2019R1A2C1007203//National Research Foundation of Korea/ ; },
abstract = {Bioactive compounds in some herbs can, directly and indirectly, protect against photoaging. We evaluated the effects of Gastrodia elata Blume (GE) and Poria cocos Wolf (PC) water extracts on ultraviolet (UV) B-induced skin lesions by acute UVB exposure in ICR mice and explored their mechanism of action. After removing the hair on the back of the mice, UVB (280-310 nm) was exposed to the back for 30 min to induce skin damage. Four UVB exposure groups were divided into the following according to the local application (1,3-butanediol extract) on the dorsal skin and oral intake (0.3 g water extract/kg body weight/day): 1,3-butanediol and cellulose(control; UV-Con), retinoic acid (positive-control; UV-Positive), PC extracts (UV-PC), and GE extracts (UV-GE). The fifth group had no UVB exposure with the same treatment as the UV-Con (Normal-control). The erythema, burns, erosion, and wounds of the UV-PC and UV-PC groups were alleviated, and the most significant improvements occurred in the UV-PC group. PC and GE reduced the thickness of the dorsal skin tissue, the penetration of mast cells, and malondialdehyde contents. The mRNA expression of TNF-α, IL-13, and IL-4, inflammatory factors, were also reduced significantly in the dorsal skin of the UV-PC and UV-GE groups. UV-PC, UV-GE, and UV-Positive showed improvements in UV-induced intestinal tissue inflammation. UV-Con deteriorated the intestinal morphology, and PC and GE alleviated it. The α-diversity of the fecal microbiota decreased in the UV-control, and UV-PC and UV-GE prevented the decrease. Fecal metagenome analysis revealed increased propionate biosynthesis in the UV-PC group but decreased lipopolysaccharide biosynthesis in the UV-PC and UV-GE groups compared to UV-Con. In conclusion, the local application and intake of PC and GE had significant therapeutic effects on acute UV-induced skin damage by reducing oxidative stress and proinflammatory cytokines, potentially promoting the gut-microbiota-gut-skin axis.},
}

@article {pmid36142684,
year = {2022},
author = {Gladkov, GV and Kimeklis, AK and Afonin, AM and Lisina, TO and Orlova, OV and Aksenova, TS and Kichko, AA and Pinaev, AG and Andronov, EE},
title = {The Structure of Stable Cellulolytic Consortia Isolated from Natural Lignocellulosic Substrates.},
journal = {International journal of molecular sciences},
volume = {23},
number = {18},
pages = {},
doi = {10.3390/ijms231810779},
pmid = {36142684},
issn = {1422-0067},
support = {18-16-00073//Russian Science Foundation/ ; },
abstract = {Recycling plant matter is one of the challenges facing humanity today and depends on efficient lignocellulose degradation. Although many bacterial strains from natural substrates demonstrate cellulolytic activities, the CAZymes (Carbohydrate-Active enZYmes) responsible for these activities are very diverse and usually distributed among different bacteria in one habitat. Thus, using microbial consortia can be a solution to rapid and effective decomposition of plant biomass. Four cellulolytic consortia were isolated from enrichment cultures from composting natural lignocellulosic substrates-oat straw, pine sawdust, and birch leaf litter. Enrichment cultures facilitated growth of similar, but not identical cellulose-decomposing bacteria from different substrates. Major components in all consortia were from Proteobacteria, Actinobacteriota and Bacteroidota, but some were specific for different substrates-Verrucomicrobiota and Myxococcota from straw, Planctomycetota from sawdust and Firmicutes from leaf litter. While most members of the consortia were involved in the lignocellulose degradation, some demonstrated additional metabolic activities. Consortia did not differ in the composition of CAZymes genes, but rather in axillary functions, such as ABC-transporters and two-component systems, usually taxon-specific and associated with CAZymes. Our findings show that enrichment cultures can provide reproducible cellulolytic consortia from various lignocellulosic substrates, the stability of which is ensured by tight microbial relations between its components.},
}

@article {pmid36142415,
year = {2022},
author = {Iacono, R and Strazzulli, A and Giglio, R and Bitetti, F and Cobucci-Ponzano, B and Moracci, M},
title = {Valorization of Biomasses from Energy Crops for the Discovery of Novel Thermophilic Glycoside Hydrolases through Metagenomic Analysis.},
journal = {International journal of molecular sciences},
volume = {23},
number = {18},
pages = {},
doi = {10.3390/ijms231810505},
pmid = {36142415},
issn = {1422-0067},
support = {PON01 01966, funded in the frame of Operative National Programme Research and Competi-tiveness 2007-2013 D. D. Prot. n. 01/Ric. 18.1.2010//Ministero dell'Università e della Ricerca Scentifica/ ; },
abstract = {The increasing interest for environmentally friendly technologies is driving the transition from fossil-based economy to bioeconomy. A key enabler for circular bioeconomy is to valorize renewable biomasses as feedstock to extract high value-added chemicals. Within this transition the discovery and the use of robust biocatalysts to replace toxic chemical catalysts play a significant role as technology drivers. To meet both the demands, we performed microbial enrichments on two energy crops, used as low-cost feed for extremophilic consortia. A culture-dependent approach coupled to metagenomic analysis led to the discovery of more than 300 glycoside hydrolases and to characterize a new α-glucosidase from an unknown hyperthermophilic archaeon. Aglu1 demonstrated to be the most active archaeal GH31 on 4Np-α-Glc and it showed unexpected specificity vs. kojibiose, revealing to be a promising candidate for biotechnological applications such as the liquefaction/saccharification of starch.},
}

@article {pmid36142289,
year = {2022},
author = {Graziano, S and Caldara, M and Gullì, M and Bevivino, A and Maestri, E and Marmiroli, N},
title = {A Metagenomic and Gene Expression Analysis in Wheat (T. durum) and Maize (Z. mays) Biofertilized with PGPM and Biochar.},
journal = {International journal of molecular sciences},
volume = {23},
number = {18},
pages = {},
doi = {10.3390/ijms231810376},
pmid = {36142289},
issn = {1422-0067},
support = {818431//European Union/ ; },
abstract = {Commodity crops, such as wheat and maize, are extremely dependent on chemical fertilizers, a practice contributing greatly to the increase in the contaminants in soil and water. Promising solutions are biofertilizers, i.e., microbial biostimulants that when supplemented with soil stimulate plant growth and production. Moreover, the biofertilizers can be fortified when (i) provided as multifunctional consortia and (ii) combined with biochar with a high cargo capacity. The aim of this work was to determine the molecular effects on the soil microbiome of different biofertilizers and delivery systems, highlight their physiological effects and merge the data with statistical analyses. The measurements of the physiological parameters (i.e., shoot and root biomass), transcriptomic response of genes involved in essential pathways, and characterization of the rhizosphere population were analyzed. The results demonstrated that wheat and maize supplemented with different combinations of selected microbial consortia and biochar have a positive effect on plant growth in terms of shoot and root biomass; the treatments also had a beneficial influence on the biodiversity of the indigenous rhizo-microbial community, reinforcing the connection between microbes and plants without further spreading contaminants. There was also evidence at the transcriptional level of crosstalk between microbiota and plants.},
}

@article {pmid36142138,
year = {2022},
author = {Borroni, D and Paytuví-Gallart, A and Sanseverino, W and Gómez-Huertas, C and Bonci, P and Romano, V and Giannaccare, G and Rechichi, M and Meduri, A and Oliverio, GW and Rocha-de-Lossada, C and On Behalf Of Lucy Consortium, },
title = {Exploring the Healthy Eye Microbiota Niche in a Multicenter Study.},
journal = {International journal of molecular sciences},
volume = {23},
number = {18},
pages = {},
doi = {10.3390/ijms231810229},
pmid = {36142138},
issn = {1422-0067},
abstract = {PURPOSE: This study aims to explore and characterize healthy eye microbiota.

METHODS: Healthy subjects older than 18 years were selected for this descriptive cross-sectional study. Samples were collected with an eSwab with 1 mL of Liquid Amies Medium (Copan Brescia, Italy). Following DNA extraction, libraries preparation, and amplification, PCR products were purified and end-repaired for barcode ligation. Libraries were pooled to a final concentration of 26 pM. Template preparation was performed with Ion Chef according to Ion 510, Ion 520, and Ion 530 Kit-Chef protocol. Sequencing of the amplicon libraries was carried out on a 520 or 530 chip using the Ion Torrent S5 system (Thermo Fisher; Waltham, MA, USA). Raw reads were analyzed with GAIA (v 2.02).

RESULTS: Healthy eye microbiota is a low-diversity microbiome. The vast majority of the 137 analyzed samples were highly enriched with Staphylococcus, whereas only in a few of them, other genera such as Bacillus, Pseudomonas, and Corynebacterium predominate. We found an average of 88 genera with an average Shannon index of 0.65.

CONCLUSION: We identified nine different ECSTs. A better understanding of healthy eye microbiota has the potential to improve disease diagnosis and personalized regimens to promote health.},
}

@article {pmid36141538,
year = {2022},
author = {Li, N and Li, H and Zhu, C and Liu, C and Su, G and Chen, J},
title = {Controlling AMR in the Pig Industry: Is It Enough to Restrict Heavy Metals?.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {18},
pages = {},
doi = {10.3390/ijerph191811265},
pmid = {36141538},
issn = {1660-4601},
support = {71790613//National Natural Science Foundation of China/ ; },
abstract = {Heavy metals have the potential to influence the transmission of antimicrobial resistance (AMR). However, the effect on AMR caused by heavy metals has not been clearly revealed. In this study, we used a microcosm experiment and metagenomics to examine whether common levels of Cu and Zn in pig manure influence AMR transmission in manured soil. We found that the abundance of 204 ARGs significantly increased after manure application, even though the manure did not contain antibiotic residuals. However, the combined addition of low Cu and Zn (500 and 1000 mg/kg, respectively) only caused 14 ARGs to significantly increase, and high Cu and Zn (1000 and 3000 mg/kg, respectively) caused 27 ARGs to significantly increase. The disparity of these numbers suggested that factors within the manure were the primary driving reasons for AMR transmission, rather than metal amendments. A similar trend was found for biocide and metal resistance genes (BMRGs) and mobile genetic elements (MGEs). This study offers deeper insights into AMR transmission in relation to the effects of manure application and heavy metals at commonly reported levels. Our findings recommend that more comprehensive measures in controlling AMR in the pig industry are needed apart from restricting heavy metal additions.},
}

@article {pmid36140733,
year = {2022},
author = {Hilt, EE and Ferrieri, P},
title = {Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases.},
journal = {Genes},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/genes13091566},
pmid = {36140733},
issn = {2073-4425},
abstract = {Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.},
}

@article {pmid36140732,
year = {2022},
author = {D'Argenio, V and Veneruso, I and Gong, C and Cecarini, V and Bonfili, L and Eleuteri, AM},
title = {Gut Microbiome and Mycobiome Alterations in an In Vivo Model of Alzheimer's Disease.},
journal = {Genes},
volume = {13},
number = {9},
pages = {},
doi = {10.3390/genes13091564},
pmid = {36140732},
issn = {2073-4425},
abstract = {Gut microbiota has emerged as an important key regulator of health and disease status. Indeed, gut microbial dysbiosis has been identified in an increasing number of diseases, including neurodegenerative disorders. Accordingly, microbial alterations have been reported also in Alzheimer's disease (AD), suggesting possible pathogenetic mechanisms contributing to the development of specific AD hallmarks and exacerbating metabolic alterations and neuroinflammation. The identification of these mechanisms is crucial to develop novel, targeted therapies and identify potential biomarkers for diagnostic purposes. Thus, the possibility to have AD in vivo models to study this microbial ecosystem represents a great opportunity for translational applications. Here, we characterized both gut microbiome and mycobiome of 3xTg-AD mice, one of the most widely used AD models, to identify specific microbial alterations with respect to the wild-type counterpart. Interestingly, we found a significant reduction of the Coprococcus and an increased abundance of Escherichia_Shigella and Barnesiella genera in the AD mice compatible with a pro-inflammatory status and the development of AD-related pathogenetic features. Moreover, the fungal Dipodascaceae family was significantly increased, thus suggesting a possible contribution to the metabolic alterations found in AD. Our data point out the strict connection between bacterial dysbiosis and AD and, even if further studies are required to clarify the underlining mechanisms, it clearly indicates the need for extensive metagenomic studies over the bacterial counterpart.},
}

@article {pmid36140548,
year = {2022},
author = {Bronkhorst, AJ and Ungerer, V and Oberhofer, A and Gabriel, S and Polatoglou, E and Randeu, H and Uhlig, C and Pfister, H and Mayer, Z and Holdenrieder, S},
title = {New Perspectives on the Importance of Cell-Free DNA Biology.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/diagnostics12092147},
pmid = {36140548},
issn = {2075-4418},
abstract = {Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.},
}

@article {pmid36140263,
year = {2022},
author = {Kovtun, AS and Averina, OV and Angelova, IY and Yunes, RA and Zorkina, YA and Morozova, AY and Pavlichenko, AV and Syunyakov, TS and Karpenko, OA and Kostyuk, GP and Danilenko, VN},
title = {Alterations of the Composition and Neurometabolic Profile of Human Gut Microbiota in Major Depressive Disorder.},
journal = {Biomedicines},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/biomedicines10092162},
pmid = {36140263},
issn = {2227-9059},
support = {20-14-00132//Russian Science Foundation/ ; },
abstract = {Major depressive disorder (MDD) is among the most prevalent mental disorders worldwide. Factors causing the pathogenesis of MDD include gut microbiota (GM), which interacts with the host through the gut-brain axis. In previous studies of GM in MDD patients, 16S rRNA sequencing was used, which provided information about composition but not about function. In our study, we analyzed whole metagenome sequencing data to assess changes in both the composition and functional profile of GM. We looked at the GM of 36 MDD patients, compared with that of 38 healthy volunteers. Comparative taxonomic analysis showed decreased abundances of Faecalibacterium prausnitzii, Roseburia hominis, and Roseburia intestinalis, and elevated abundances of Escherichia coli and Ruthenibacterium lactatiformans in the GM of MDD patients. We observed decreased levels of bacterial genes encoding key enzymes involved in the production of arginine, asparagine, glutamate, glutamine, melatonin, acetic, butyric and conjugated linoleic acids, and spermidine in MDD patients. These genes produced signature pairs with Faecalibacterium prausntizii and correlated with decreased levels of this species in the GM of MDD patients. These results show the potential impact of the identified biomarker bacteria and their metabolites on the pathogenesis of MDD, and should be confirmed in future metabolomic studies.},
}

@article {pmid36139998,
year = {2022},
author = {Alvarado, AC and Chekabab, SM and Predicala, BZ and Korber, DR},
title = {Impact of Raised without Antibiotics Measures on Antimicrobial Resistance and Prevalence of Pathogens in Sow Barns.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
doi = {10.3390/antibiotics11091221},
pmid = {36139998},
issn = {2079-6382},
support = {20170069//Saskatchewan Ministry of Agriculture/ ; },
abstract = {The growing concern over the emergence of antimicrobial resistance (AMR) in animal production as a result of extensive and inappropriate antibiotic use has prompted many swine farmers to raise their animals without antibiotics (RWA). In this study, the impact of implementing an RWA production approach in sow barns on actual on-farm antibiotic use, the emergence of AMR, and the abundance of pathogens was investigated. Over a 13-month period, fecal and nasopharynx samples were collected at 3-month intervals from sows raised in RWA barns and sows in conventional barns using antibiotics in accordance with the new regulations (non-RWA). Whole genome sequencing (WGS) was used to determine the prevalence of AMR and the presence of pathogens in those samples. Records of all drug use from the 13-month longitudinal study indicated a significant reduction in antimicrobial usage in sows from RWA barns compared to conventional non-RWA barns. Antifolates were commonly administered to non-RWA sows, whereas β-lactams were widely used to treat sows in RWA barns. Metagenomic analyses demonstrated an increased abundance of pathogenic Actinobacteria, Firmicutes, and Proteobacteria in the nasopharynx microbiome of RWA sows relative to non-RWA sows. However, WGS analyses revealed that the nasal microbiome of sows raised under RWA production exhibited a significant increase in the frequency of resistance genes coding for β-lactams, MDR, and tetracycline.},
}

@article {pmid36138831,
year = {2022},
author = {Garralda, MD and Weiner, S and Arensburg, B and Maureille, B and Vandermeersch, B},
title = {Dental Paleobiology in a Juvenile Neanderthal (Combe-Grenal, Southwestern France).},
journal = {Biology},
volume = {11},
number = {9},
pages = {},
doi = {10.3390/biology11091352},
pmid = {36138831},
issn = {2079-7737},
support = {00//Ministerio de Educación y Ciencia, Spain/ ; },
abstract = {Combe-Grenal site (Southwest France) was excavated by F. Bordes between 1953 and 1965. He found several human remains in Mousterian levels 60, 39, 35 and especially 25, corresponding to MIS 4 (~75-70/60 ky BP) and with Quina Mousterian lithics. One of the fossils found in level 25 is Combe-Grenal IV, consisting of a fragment of the left corpus of a juvenile mandible. This fragment displays initial juvenile periodontitis, and the two preserved teeth (LLP4 and LLM1) show moderate attrition and dental calculus. The SEM tartar analysis demonstrates the presence of cocci and filamentous types of bacteria, the former being more prevalent. This result is quite different from those obtained for the two adult Neanderthals Kebara 2 and Subalyuk 1, where more filamentous bacteria appear, especially in the Subalyuk 1 sample from Central Europe. These findings agree with the available biomedical data on periodontitis and tartar development in extant individuals, despite the different environmental conditions and diets documented by numerous archeological, taphonomical and geological data available on Neanderthals and present-day populations. New metagenomic analyses are extending this information, and despite the inherent difficulties, they will open important perspectives in studying this ancient human pathology.},
}

@article {pmid36138466,
year = {2022},
author = {Keller-Costa, T and Kozma, L and Silva, SG and Toscan, R and Gonçalves, J and Lago-Lestón, A and Kyrpides, NC and Nunes da Rocha, U and Costa, R},
title = {Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {151},
pmid = {36138466},
issn = {2049-2618},
support = {CEECIND/00788/2017//Fundação para a Ciência e a Tecnologia/ ; UIDB/04565/2020, UIDP/04565/2020, LA/P/0140/2020//Fundação para a Ciência e a Tecnologia/ ; UIDB/04565/2020, UIDP/04565/2020, LA/P/0140/2020//Fundação para a Ciência e a Tecnologia/ ; EXPL/MAR-EST/1664/2013//Fundação para a Ciência e a Tecnologia/ ; UIDB/04565/2020, UIDP/04565/2020, LA/P/0140/2020//Fundação para a Ciência e a Tecnologia/ ; FA_05_2017_032//Fundo Azul programme of the Direção-Geral de Política do Mar/ ; FA_05_2017_032//Fundo Azul programme of the Direção-Geral de Política do Mar/ ; VH-NG-1248 Micro 'Big Data'//Helmholtz Association/ ; VH-NG-1248 Micro 'Big Data'//Helmholtz Association/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; },
abstract = {BACKGROUND: The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater.

RESULTS: Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae. Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae, may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae, which lack such capacity.

CONCLUSION: This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae, Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large. Video Abstract.},
}

@article {pmid36137486,
year = {2022},
author = {Afridi, MS and Fakhar, A and Kumar, A and Ali, S and Medeiros, FHV and Muneer, MA and Ali, H and Saleem, M},
title = {Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering.},
journal = {Microbiological research},
volume = {265},
number = {},
pages = {127199},
doi = {10.1016/j.micres.2022.127199},
pmid = {36137486},
issn = {1618-0623},
abstract = {The rhizosphere is a narrow and dynamic region of plant root-soil interfaces, and it's considered one of the most intricate and functionally active ecosystems on the Earth, which boosts plant health and alleviates the impact of biotic and abiotic stresses. Improving the key functions of the microbiome via engineering the rhizosphere microbiome is an emerging tool for improving plant growth, resilience, and soil-borne diseases. Recently, the advent of omics tools, gene-editing techniques, and sequencing technology has allowed us to unravel the entangled webs of plant-microbes interactions, enhancing plant fitness and tolerance to biotic and abiotic challenges. Plants secrete signaling compounds with low molecular weight into the rhizosphere, that engage various species to generate a massive deep complex array. The underlying principle governing the multitrophic interactions of the rhizosphere microbiome is yet unknown, however, some efforts have been made for disease management and agricultural sustainability. This review discussed the intra- and inter- microbe-microbe and microbe-animal interactions and their multifunctional roles in rhizosphere microbiome engineering for plant health and soil-borne disease management. Simultaneously, it investigates the significant impact of immunity utilizing PGPR and cover crop strategy in increasing rhizosphere microbiome functions for plant development and protection using omics techniques. The ecological engineering of rhizosphere plant interactions could be used as a potential alternative technology for plant growth improvement, sustainable disease control management, and increased production of economically significant crops.},
}

@article {pmid36136668,
year = {2022},
author = {Bennato, F and Martino, C and Di Domenico, M and Ianni, A and Chai, B and Di Marcantonio, L and Cammà, C and Martino, G},
title = {Metagenomic Characterization and Volatile Compounds Determination in Rumen from Saanen Goat Kids Fed Olive Leaves.},
journal = {Veterinary sciences},
volume = {9},
number = {9},
pages = {},
doi = {10.3390/vetsci9090452},
pmid = {36136668},
issn = {2306-7381},
support = {F/170011/01-05/X42//Ministry of Economic Development/ ; },
abstract = {The accumulation and disposal of by-products deriving from the agro-food industry represents a problem both from an economic and environmental point of view. The use of these matrices in zootechnical nutrition could represent a feasible solution. The aim of the study was to examine the effect of a diet containing olive leaves (OL), a by-product of the olive industry, on the ruminal microbial community of Saanen goat kids and on volatile organic compounds (VOCs) produced during the digestion. Twenty goat kids were randomly divided into two groups of ten goat kids each. The control group (CTR) was fed with a standard diet, while the experimental group (OL+) received a custom-formulated diet containing 10 % OL on a dry matter (DM) basis. After 30 days of trial, genomic DNA was extracted from the rumen liquor and prepared for 16S rRNA-gene sequencing to characterize the rumen microbiota; furthermore, rumen VOCs were also characterized by solid-phase microextraction coupled with gas chromatography-mass spectrometry. The Shannon's alpha index was not significantly different between the two groups, on the contrary, Bray-Curtis (p < 0.01) and Jaccard (p < 0.01) distances evidenced that feed affected microbial community. Eleven genera were influenced by OL supplementation, with a significant increase (p < 0.05) in Paludibacter, Fibrobacter, Sphaerochaeta Christensenella, Rikenella, Oligosphaera, Candidatus Endomicrobium, Anaerovorax, and Atopobium was observed, while the percentages of Bacteroides and Selenomonas were reduced (p < 0.05). Differences were also observed between the two groups at the family level (p < 0.004). Fibrobacteriaceae, Christensenellaceae, Coriobacteriaceae, Oligosphaeraceae, Candidatus Endomicrobium, and Planctomycetaceae were significantly higher (p < 0.05) in goat kids fed OL diet compared to CTR, while the levels of other identified families, Succinivibrionaceae and Bifidobacteriaceae, were opposite (p < 0.05). Finally, results showed that the main phyla in both groups were Bacteroidetes and Firmicutes; however, no significant differences in the relative abundance of any phyla were observed between the two groups. In addition to what has been reported, the analysis of VOCs at the rumen level showed the ability of the OL integration to induce an increase in hexanoic acid and a parallel decrease in decanal. Furthermore, only in OL+ samples there was the accumulation of α-terpineol to which a wide range of interesting biological properties is attributed. The presence of VOCs associated with health status suggests a favorable role of OL in preserving and improving animal welfare.},
}

@article {pmid36136471,
year = {2022},
author = {Ma, C and Ma, P and He, Z and Mi, X},
title = {A Combined Catalytic Ozonation-MBR Approach to Remove Contaminants from the Mature Landfill Leachate in the Yellow River Basin.},
journal = {Toxics},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/toxics10090505},
pmid = {36136471},
issn = {2305-6304},
abstract = {The mature landfill leachate (MLL) is characterized by a large number of fulvic acids and humic acids, which is refractory organic matter and can be cleaned by ozone oxidation. However, the poor property of mass transfer prohibits the widespread use of ozone oxidation in actual leachate treatment. Meanwhile, some combined processes are adopted to treat the mature landfill leachate, which places catalytic ozonation before the membrane bioreactor (MBR) process to enhance the biodegradability of MLL. Thus, this research is conducted to investigate the practicability of applying nano-Fe3O4 loaded cow-dung ash (Fe3O4@CDA) and biological post-treatment with MBR for the effective removal of pollutants from MLL and puts forward the variation of organics in leachate between catalytic ozonation and MBR. The addition of catalytic ozonation not only improved the removal of hazardous organics but also enhanced the biodegradability of the leachate and favored the subsequent MBR process. Chemical oxygen demand (COD) removal in the catalytic ozonation step was optimized, and 53% removal was obtained at pH = 7, catalyst dosage = 1.0 g/L, and O3 dosage = 3.0 g/L. After the MBR process, COD in effluent stabilized in the range of 57.85-65.38 mg/L, and the variation range of the ammonia nitrogen (NH3-N) concentration was 5.98-10.24 mg/L. The catalytic ozonation-MBR integrated process showed strong feasibility in dealing with the biologically pre-treated leachate.},
}

@article {pmid36135885,
year = {2022},
author = {Li, C and Maqbool, T and Kang, H and Zhang, Z},
title = {In-Situ Sludge Reduction Performance and Mechanism in Sulfidogenic Anoxic-Oxic-Anoxic Membrane Bioreactors.},
journal = {Membranes},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/membranes12090865},
pmid = {36135885},
issn = {2077-0375},
support = {52170041//National Natural Science Foundation of China/ ; },
abstract = {The excess sludge generated from the activated sludge process remains a big issue. Sustainable approaches that achieve in situ sludge reduction with satisfactory effluent quality deserve attention. This study explored the sludge reduction performance of sulfidogenic anoxic-oxic-anoxic (AOA) membrane bioreactors. The dynamics of the microbial community and metabolic pathways were further analyzed to elucidate the internal mechanism of sludge reduction. Compared with the conventional anoxic-oxic-oxic membrane bioreactor (MBRcontrol), AOAS150 (150 mg/L SO42- in the membrane tank) and AOAS300 (300 mg/L SO42- in the membrane tank) reduced biomass production by 40.39% and 47.45%, respectively. The sulfide reduced from sulfate could enhance the sludge decay rate and decrease sludge production. Extracellular polymeric substances (EPSs) destruction and aerobic lysis contributed to sludge reduction in AOA bioreactors. The relative abundance of Bacteroidetes (phylum), sulfate-reducing bacteria (SRB, genus), and Ignavibacterium (genus) increased in AOA bioreactors compared with MBRcontrol. Our metagenomic analysis indicated that the total enzyme-encoding genes involved in glycolysis, denitrification, and sulfate-reduction processes decreased over time in AOAS300 and were lower in AOAS300 than AOAS150 at the final stage of operation. The excess accumulation of sulfide in AOAS300 may inactive the functional bacteria, and sulfide inhibition induced sludge reduction.},
}

@article {pmid36135710,
year = {2022},
author = {Tan, Y and Du, H and Zhang, H and Fang, C and Jin, G and Chen, S and Wu, Q and Zhang, Y and Zhang, M and Xu, Y},
title = {Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0184422},
doi = {10.1128/spectrum.01844-22},
pmid = {36135710},
issn = {2165-0497},
abstract = {Fermented foods often have attractive flavor characteristics to meet various human demands. An ever-challenging target is the production of fermented foods with equal flavor profiles outside the product's origin. However, the formation of geography-dependent flavor in high-complexity fermentations remains poorly understood. Here, taking Chinese liquor (baijiu) fermentation as an example, we collected 403 samples from 9 different locations in China across a latitude range of 27°N to 37°N. We revealed and validated the geography-dependent flavor formation patterns by using culture-independent (metabolomics, metagenomics, and metatranscriptomics) and culture-dependent tools. We found that the baijiu microbiomes along with their metabolites were flavor related and geography dependent. The geographical characteristics were determined mainly by 20 to 40 differentiated chemical markers in metabolites and the latitude-dependent fungal structure of the microbiome. About 48 to 156 core microbiota members out of 735 bacterial genera and 290 fungal genera contributed to the chemical markers. The contributions of both fungi and bacteria were greater than those from either bacteria or fungi alone. Representatively, we revealed that dynamic interdependent interactions between yeasts and Lactobacillus facilitated the metabolism of heterocyclic flavor chemicals such as 2-acetylpyrrole, 2,3,5-trimethylpyrazine, and 2-acetylfuran. Moreover, we found that the intraspecific genomic diversity and microbial structure were two biotic factors that contributed to dynamic microbiome assembly. Based on the assembly pattern, adjusting the composition and distribution of initial species was one option to regulate the formation of diverse flavor characteristics. Our study provided a rationale for developing a microbiome design to achieve a defined flavor goal. IMPORTANCE People consume many spontaneously fermented foods and beverages with different flavors on a daily basis. One crucial and hotly discussed question is how to reproduce fermented food flavor without geographical limitations to meet diverse human demands. The constantly enriched knowledge of the microbial contribution to fermented flavor offers valuable insights into flavor biotechnological development. However, we still have a poor understanding of what factors limit the reproduction of fermented flavor outside the product's origin in high-complexity spontaneous fermentations. Here, taking baijiu fermentation as an example, we revealed that geography-dependent flavor was contributed mainly by fungus-bacterium cooperative metabolism. The distinct initial microbial composition, distribution, and intraspecific genomic diversity limited reproducible microbial interactions and metabolism in different geographical areas. The abundant microbial resources and predicted fungus-bacterium interactions found in baijiu fermentation enable us to design a synthetic microbial community to reproduce desired flavor profiles in the future.},
}

@article {pmid36135388,
year = {2022},
author = {Peroumal, D and Sahu, SR and Kumari, P and Utkalaja, BG and Acharya, N},
title = {Commensal Fungus Candida albicans Maintains a Long-Term Mutualistic Relationship with the Host To Modulate Gut Microbiota and Metabolism.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0246222},
doi = {10.1128/spectrum.02462-22},
pmid = {36135388},
issn = {2165-0497},
abstract = {Candida albicans survives as a commensal fungus in the gastrointestinal tract, and that its excessive growth causes infections in immunosuppressed individuals is widely accepted. However, any mutualistic relationship that may exist between C. albicans and the host remains undetermined. Here, we showed that a long-term feeding of C. albicans does not cause any noticeable infections in the mouse model. Our 16S and 18S ribosomal DNA (rDNA) sequence analyses suggested that C. albicans colonizes in the gut and modulates microbiome dynamics, which in turn mitigates high-fat-diet-induced uncontrolled body weight gain and metabolic hormonal imbalances. Interestingly, adding C. albicans to a nonobesogenic diet stimulated the appetite-regulated hormones and helped the mice maintain a healthy body weight. In concert, our results suggest a mutualism between C. albicans and the host, contrary to the notion that C. albicans is always an adversary and indicating it can instead be a bona fide admirable companion of the host. Finally, we discuss its potential translational implication as a probiotic, especially in obese people or people dependent on high-fat calorie intakes to manage obesity associated complications. IMPORTANCE Candida albicans is mostly considered an opportunistic pathogen that causes fetal systemic infections. However, this study demonstrates that in its commensal state, it maintains a long-term mutualistic relationship with the host and regulates microbial dynamics in the gut and host physiology. Thus, we concluded that C. albicans is not always an adversary but rather can be a bona fide admirable companion of the host. More importantly, as several genomic knockout strains of C. albicans were shown to be avirulent, such candidate strains may be explored further as preferable probiotic isolates to control obesity.},
}

@article {pmid36135379,
year = {2022},
author = {Du, J and Zhang, J and Zhang, D and Zhou, Y and Wu, P and Ding, W and Wang, J and Ouyang, C and Yang, Q},
title = {Background Filtering of Clinical Metagenomic Sequencing with a Library Concentration-Normalized Model.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0177922},
doi = {10.1128/spectrum.01779-22},
pmid = {36135379},
issn = {2165-0497},
abstract = {Metagenomic next-generation sequencing (mNGS) can accurately detect pathogens in clinical samples. However, wet-lab contamination constrains mNGS analysis and may result in erroneous interpretation of results. Many existing methods rely on large-scale observational microbiome studies and may not be applicable to clinical mNGS tests. By generation of a pretrained profile of common laboratory contaminants, we developed an mNGS noise-filtering model based on the inverse linear relationship between microbial sequencing reads and sample library concentration, named the background elimination and correction by library concentration-normalized (BECLEAN) model. Its efficacy was evaluated with bacteria- and yeast-spiked samples and 28 cerebrospinal fluid (CSF) specimens. The diagnostic accuracy, precision, sensitivity, and specificity of BECLEAN with reference to conventional methods and diagnosis were 92.9%, 86.7%, 100%, and 86.7%, respectively. BECLEAN led to a dramatic reduction of background noise without affecting the true-positive rate and thus can provide a time-saving and convenient tool in various clinical settings. IMPORTANCE Most of the existing methods to remove wet-lab contamination rely on large-scale observational microbiome studies and may not be applicable to clinical mNGS testing in individual cases. In clinical settings, only a handful of samples might be sequenced in a run. The lab-specific microbiome can complicate existing statistical approaches for removing contamination from small-scale clinical metagenomic sequencing data sets; thus, use of a preliminary lab-specific training set is necessary. Our study provides a rapid and accurate background-filtering tool for clinical metagenomic sequencing by generation of a pretrained profile of common laboratory contaminants. Notably, our work demonstrates that the inverse linear relationship between microbial sequencing reads and library concentration can serve to identify true contaminants and evaluate the relative abundance of a taxon in samples by comparing the observed microbial reads to the model-predicted value. Our findings extend the previously published research and demonstrate confirmatory results in clinical settings.},
}

@article {pmid36131174,
year = {2022},
author = {Su, C and Zhou, X and Lu, P and Dai, X and Chen, Z and Liang, B and Tian, Y and Chen, M},
title = {Role of coke media strategy in an adsorption-biological coupling technology for wastewater treatment performance, microbial community, and metabolic pathways features.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {36131174},
issn = {1614-7499},
abstract = {With the increase of wastewater discharge, the requirement of wastewater treatment technology is gradually increased. How to treat wastewater economically, while making the treatment process short, easy to manage and low running cost, is the focus of attention. Adsorption-biological coupling technology could make adsorption and biodegradation complement each other, which has coupled accumulation effect. In this study, with coke as the adsorbent, the efficiency of the adsorption-biological coupling reactor on the treatment of total phosphorus (TP), chemical oxygen demand (COD), and ammonia nitrogen (NH3-N) in domestic wastewater under different influent modes was investigated. Meanwhile, microbial community and metabolic pathways analysis of the reactor were carried out. Results showed that when the influent modes of the coupling reactor was once a day and the daily sewage treatment capacity was 2 L, the treatment efficiency of TP, COD, and NH3-N was the best. The removal rate of TP and NH3-N was 87.96% and 96.14%, respectively. The dominant phylum was Proteobacteria (39.84-44.49%), and the dominant genus was Sphingomonas (4.27-7.16%), and Gemmatimonas (1.27-3.58%). According to the metagenomic analysis, carbon metabolism process was evenly distributed in U (upper), M (middle), and L (lower) layers of the coupling reactor. Phosphate metabolism was mainly in the U layer at first, then in the M and L layers gradually. Carbon metabolism and phosphate metabolism provided sufficient energy for microbial degradation of pollutants. Nitrogen removal in the reactor mainly happened in the S and Z layers by nitrification (M00528) and denitrification (M00529), respectively.},
}

@article {pmid36130883,
year = {2022},
author = {Kato-Kogoe, N and Kamiya, K and Sakaguchi, S and Omori, M and Komori, E and Kudo, A and Nakamura, S and Nakano, T and Ueno, T and Tamaki, J and Hoshiga, M},
title = {Salivary Microbiota Associated with Peripheral Microvascular Endothelial Dysfunction.},
journal = {Journal of atherosclerosis and thrombosis},
volume = {},
number = {},
pages = {},
doi = {10.5551/jat.63681},
pmid = {36130883},
issn = {1880-3873},
abstract = {AIMS: Oral health is associated with atherosclerotic cardiovascular disease (ACVD). We previously identified the salivary microbiota characteristics of patients with ACVD. However, whether salivary microbiota is characteristic under impaired vascular endothelial function before ACVD onset remains unclear. Therefore, we aimed to evaluate the characteristics of salivary microbiota associated with peripheral microvascular endothelial dysfunction.

METHODS: We collected saliva samples from 172 community-dwelling elderly individuals without a history of ACVD and performed 16S rRNA metagenomic analysis. We assessed the peripheral microvascular endothelial function using reactive hyperemia index (RHI) and compared the salivary microbiota in the groups with normal (RHI ≥ 2.10), borderline, and abnormal (RHI ＜1.67) peripheral endothelial function. Furthermore, we applied machine learning techniques to evaluate whether salivary microbiota could discriminate between individuals with normal and abnormal endothelial function.

RESULTS: The number of operational taxonomic units (OTUs) was higher in the abnormal group than in the normal group (p=0.037), and differences were found in the overall salivary microbiota structure (unweighted UniFrac distances, p=0.038). The linear discriminant analysis (LDA) effect size (LEfSe) algorithm revealed several significantly differentially abundant bacterial genera between the two groups. An Extra Trees classifier model was built to discriminate between groups with normal and abnormal vascular endothelial function based on the microbial composition at the genus level (AUC=0.810).

CONCLUSIONS: The salivary microbiota in individuals with endothelial dysfunction was distinct from that in individuals with normal endothelial function, indicating that the salivary microbiota may be related to endothelial function.},
}

@article {pmid35715385,
year = {2022},
author = {Gronniger, JL and Wang, Z and Brandt, GR and Ward, CS and Tsementzi, D and Mu, H and Gu, J and Johnson, ZI and Konstantinidis, KT and Hunt, DE},
title = {Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables.},
journal = {Environmental microbiology},
volume = {24},
number = {9},
pages = {4167-4177},
doi = {10.1111/1462-2920.16086},
pmid = {35715385},
issn = {1462-2920},
support = {ICER 2033934//National Science Foundation/ ; OCE 1416665//National Science Foundation/ ; OCE 1416673//National Science Foundation/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; },
mesh = {Metagenome ; *Microbiota/genetics ; Oceans and Seas ; Phytoplankton ; },
abstract = {Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host-associated and engineered systems. In spite of global change both altering environmental averages and increasing extreme events, there has been relatively little research into the causes, persistence and population-level impacts of disturbance in the dynamic coastal ocean. Here, we utilize 3 years of observations from a coastal time series to identify disturbances based on the largest week-over-week changes in the microbiome (i.e. identifying disturbance as events that alter the community composition). In general, these microbiome disturbances were not clearly linked to specific environmental factors and responsive taxa largely differed, aside from SAR11, which generally declined. However, several disturbance metagenomes identified increased phage-associated genes, suggesting that unexplained community shifts might be caused by increased mortality. Furthermore, a category 1 hurricane, the only event that would likely be classified a priori as an environmental disturbance, was not an outlier in microbiome composition, but did enhance a bloom in seasonally abundant phytoplankton. Thus, as extreme environmental changes intensify, assumptions of what constitutes a disturbance should be re-examined in the context of ecological history and microbiome responses.},
}

Metagenome
*Microbiota/genetics
Oceans and Seas
Phytoplankton

@article {pmid36130784,
year = {2022},
author = {Brown, MA and Jabeen, M and Bharj, G and Hinks, TSC},
title = {Non-typeable Haemophilus influenzae airways infection: the next treatable trait in asthma?.},
journal = {European respiratory review : an official journal of the European Respiratory Society},
volume = {31},
number = {165},
pages = {},
doi = {10.1183/16000617.0008-2022},
pmid = {36130784},
issn = {1600-0617},
abstract = {Asthma is a complex, heterogeneous condition that affects over 350 million people globally. It is characterised by bronchial hyperreactivity and airways inflammation. A subset display marked airway neutrophilia, associated with worse lung function, higher morbidity and poor response to treatment. In these individuals, recent metagenomic studies have identified persistent bacterial infection, particularly with non-encapsulated strains of the Gram-negative bacterium Haemophilus influenzae. Here we review knowledge of non-typeable H. influenzae (NTHi) in the microbiology of asthma, the immune consequences of mucosal NTHi infection, various immune evasion mechanisms, and the clinical implications of NTHi infection for phenotyping and targeted therapies in neutrophilic asthma. Airway neutrophilia is associated with production of neutrophil chemokines and proinflammatory cytokines in the airways, including interleukin (IL)-1β, IL-6, IL-8, IL-12, IL-17A and tumour necrosis factor. NTHi adheres to and invades the lower respiratory tract epithelium, inducing the NLR family pyrin domain containing 3 (NLRP3) and absent in melanoma 2 (AIM2) inflammasomes. NTHi reduces expression of tight-junction proteins, impairing epithelial integrity, and can persist intracellularly. NTHi interacts with rhinoviruses synergistically via upregulation of intracellular cell adhesion molecule 1 and promotion of a neutrophilic environment, to which NTHi is adapted. We highlight the clinical relevance of this emerging pathogen and its relevance for the efficacy of long-term macrolide therapy in airways diseases, we identify important unanswered questions and we propose future directions for research.},
}

@article {pmid36130161,
year = {2022},
author = {Wang, L and Soto, A and Remue, L and Rosales Rosas, AL and De Coninck, L and Verwimp, S and Bouckaert, J and Vanwinkel, M and Matthijnssens, J and Delang, L},
title = {First Report of Mutations Associated With Pyrethroid (L1014F) and Organophosphate (G119S) Resistance in Belgian Culex (Diptera: Culicidae) Mosquitoes.},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjac138},
pmid = {36130161},
issn = {1938-2928},
support = {C14/20/108//KU Leuven/ ; },
abstract = {The emergence of West Nile virus and Usutu virus in Europe poses a significant risk to public health. In the absence of efficient antiviral therapy or vaccine candidates, the only strategy to control these arboviruses is to target the Culex (Diptera: Culicidae) mosquito vector. However, the selection pressure caused by exposure to insecticides for vector control or agricultural pest control can lead to insecticide resistance, thereby reducing the efficacy of insecticide-based vector control interventions. In Culex mosquitoes, two of the most common amino acid substitutions associated with insecticide resistance are the kdr L1014F in voltage gated sodium channels and G119S in acetylcholinesterase. In this study, Culex pipiens biotype pipiens, Culex torrentium, and Culex modestus were sampled from 2019 to 2021 in three distinct environmental habitats (urban, peri-urban, and agricultural) in and around the city of Leuven, Belgium. Individual mosquitoes were screened for two mutations resulting in L1014F and G119S amino acid substitutions. Both mutations were observed in Cx. pipiens and Cx. modestus but not in Cx. torrentium mosquitoes across the four collection sites. Furthermore, multi-resistance or cross-resistance in Cx. pipiens could be a threat in these areas, as both mutations were observed at low frequencies. These results provide the first report of kdr L1014F and ace-1 G119S resistance mutations in Cx. pipiens and Cx. modestus mosquitoes from Belgium, highlighting the importance of mosquito surveillance to design effective arbovirus outbreak control strategies.},
}

@article {pmid36130056,
year = {2022},
author = {Ziemski, M and Adamov, A and Kim, L and Flörl, L and Bokulich, NA},
title = {Reproducible acquisition, management, and meta-analysis of nucleotide sequence (meta)data using q2-fondue.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btac639},
pmid = {36130056},
issn = {1367-4811},
abstract = {MOTIVATION: The volume of public nucleotide sequence data has blossomed over the past two decades, and is ripe for re- and meta-analyses to enable novel discoveries. However, reproducible re-use and management of sequence datasets and associated metadata remain critical challenges. We created the open source Python package q2-fondue to enable user-friendly acquisition, re-use, and management of public sequence (meta)data while adhering to open data principles.

RESULTS: q2-fondue allows fully provenance-tracked programmatic access to and management of data from the NCBI Sequence Read Archive (SRA). Unlike other packages allowing download of sequence data from the SRA, q2-fondue enables full data provenance tracking from data download to final visualization, integrates with the QIIME 2 ecosystem, prevents data loss upon space exhaustion, and allows download of (meta)data given a publication library. To highlight its manifold capabilities, we present executable demonstrations using publicly available amplicon, whole genome, and metagenome datasets.

AVAILABILITY: q2-fondue is available as an open-source BSD-3-licensed Python package at https://github.com/bokulich-lab/q2-fondue. Usage tutorials are available in the same repository. All Jupyter notebooks used in this article are available under https://github.com/bokulich-lab/q2-fondue-examples.

SUPPLEMENTARY INFORMATION: An introductory tutorial with background information and examples for the usage of q2-fondue can be accessed at https://github.com/bokulich-lab/q2-fondue/blob/main/tutorial/tutorial.md.},
}

@article {pmid36129562,
year = {2022},
author = {Boros, Á and Albert, M and Urbán, P and Herczeg, R and Gáspár, G and Balázs, B and Cságola, A and Pankovics, P and Gyenesei, A and Reuter, G},
title = {Unusual "Asian-origin" 2c to 2b point mutant canine parvovirus (Parvoviridae) and canine astrovirus (Astroviridae) co-infection detected in vaccinated dogs with an outbreak of severe haemorrhagic gastroenteritis with high mortality rate in Hungary.},
journal = {Veterinary research communications},
volume = {},
number = {},
pages = {},
pmid = {36129562},
issn = {1573-7446},
support = {FK134311//Hungarian Scientific Research Fund/ ; FK134311//Hungarian Scientific Research Fund/ ; FK134311//Hungarian Scientific Research Fund/ ; FK134311//Hungarian Scientific Research Fund/ ; FK134311//Hungarian Scientific Research Fund/ ; FK134311//Hungarian Scientific Research Fund/ ; FK134311//Hungarian Scientific Research Fund/ ; FK134311//Hungarian Scientific Research Fund/ ; FK134311//Hungarian Scientific Research Fund/ ; FK134311//Hungarian Scientific Research Fund/ ; },
abstract = {In this study, the aetiological background of an outbreak of severe haemorrhagic gastroenteritis (HGE) in a colony of purebred Jack Russell Terriers vaccinated against CPV-2 in Hungary was investigated. Canine parvovirus 2 (CPV-2, Parvoviridae) and canine astrovirus (CaAstV, Astroviridae) co-infection was identified by viral metagenomics and next-generation sequencing (VM-NGS) methods from a rectal swab of an affected 7-week-old puppy. The complete coding sequence of CPV-2 strain FR1/CPV2-2021-HUN (ON733252) and the complete genome of CaAstV strain FR1/CaAstV-2021-HUN (ON733251) were determined by VM-NGS and PCR methods. Results of sequence and phylogenetic analyses showed that CPV-2 strain FR1/CPV2-2021-HUN was different from the applied vaccine strains and previously identified strains from Hungary but showed high sequence identity (> 99.8%) and close phylogenetic relationship to recently described "Asian-origin" CPV-2c strains from Italy. But, based on the single amino acid difference on position 426 of VP2 (Glu/Asp) between the study strain and the closest relatives, FR1/CPV2-2021-HUN belonged to the 2b antigenic type rather than 2c. The CaAstV strain FR1/CaAstV-2021-HUN showed close relationship with a CaAstV strain identified previously from a diarrhoeic dog in Hungary. Both viruses were continuously detectable by PCR in additional enteric samples, and the CPV-2 could also be detected in several (n = 32) tissue samples from 9 affected deceased puppies. Further comparative studies are necessary to confirm the role of the point mutation causing the change in the antigenic type of this "Asian-origin" CPV-2 and/or the role of CaAstV co-infection in the development and/or severity of (haemorrhagic) gastroenteritis among dogs vaccinated against CPV-2.},
}

@article {pmid36128620,
year = {2022},
author = {Li, Y and Sun, H and Huang, Y and Yin, A and Zhang, L and Han, J and Lyu, Y and Xu, X and Zhai, Y and Sun, H and Wang, P and Zhao, J and Sun, S and Dong, H and Zhu, F and Wang, Q and Augusto Rohde, L and Xie, X and Sun, X and Xiong, L},
title = {Gut metagenomic characteristics of ADHD reveal low Bacteroides ovatus-associated host cognitive impairment.},
journal = {Gut microbes},
volume = {14},
number = {1},
pages = {2125747},
doi = {10.1080/19490976.2022.2125747},
pmid = {36128620},
issn = {1949-0984},
abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a highly heterogeneous psychiatric disorder that can have three phenotypical presentations: inattentive (I-ADHD), hyperactive-impulsive (HI-ADHD), and combined (C-ADHD). Environmental factors correlated with the gut microbiota community have been implicated in the development of ADHD. However, whether different ADHD symptomatic presentations are associated with distinct microbiota compositions and whether patients could benefit from the correction of aberrant bacterial colonization are still largely unclear. We carried out metagenomic shotgun analysis with 207 human fecal samples to characterize the gut microbial profiles of patients with ADHD grouped according to their phenotypical presentation. Then, we transplanted the candidate low-abundance bacteria identified in patient subgroups into ADHD rats and evaluated ADHD-associated behaviors and neuronal activation in these rats. Patients with C-ADHD had a different gut microbial composition from that of healthy controls (HCs) (p = .02), but not from that of I-ADHD patients. Eight species became progressively attenuated or enriched when comparing the compositions of HCs to those of I-ADHD and C-ADHD; in particular, the abundance of Bacteroides ovatus was depleted in patients with C-ADHD. In turn, Bacteroides ovatus supplementation ameliorated spatial working memory deficits and reversed θ electroencephalogram rhythm alterations in ADHD rats. In addition, Bacteroides ovatus induced enhanced neuronal activation in the hippocampal CA1 subregion. These findings indicate that gut microbial characteristics that are unique to patients with C-ADHD may be masked when considering a more heterogeneous group of patients. We link the gut microbiota to brain function in an ADHD animal model, suggesting the relevance of testing a potential bacteria-based intervention for some aspects of ADHD.},
}

@article {pmid36126709,
year = {2022},
author = {Loiola, M and Silva, AET and Krull, M and Barbosa, FA and Galvão, EH and Patire, VF and Cruz, ICS and Barros, F and Hatje, V and Meirelles, PM},
title = {Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {158863},
doi = {10.1016/j.scitotenv.2022.158863},
pmid = {36126709},
issn = {1879-1026},
abstract = {Shrimp farming is blooming worldwide, posing a severe threat to mangroves and its multiple goods and ecosystem services. Several studies reported the impacts of aquaculture on mangrove biotic communities, including microbiomes. However, little is known about how mangrove soil microbiomes would change in response to mangrove forest recolonization. Using genome-resolved metagenomics, we compared the soil microbiome of mangrove forests (both with and without the direct influence of shrimp farming effluents) with active shrimp farms and mangroves under a recolonization process. We found that the structure and composition of active shrimp farms microbial communities differ from the control mangrove forests, mangroves under the impact of the shrimp farming effluents, and mangroves under recolonization. Shrimp farming ponds microbiomes have lower microbial diversity and are dominated by halophilic microorganisms, presenting high abundance of multiple antibiotic resistance genes. On the other hand, control mangrove forests, impacted mangroves (exposed to the shrimp farming effluents), and recolonization ponds were more diverse, with a higher abundance of genes related to carbon mobilization. Our data also indicated that the microbiome is recovering in the mangrove recolonization ponds, performing vital metabolic functions and functionally resembling microbiomes found in those soils of neighboring control mangrove forests. Despite highlighting the damage caused by the habitat changes in mangrove soil microbiome community and functioning, our study sheds light on these systems incredible recovery capacity. Our study shows the importance of natural mangrove forest recovery, enhancing ecosystem services by the soil microbial communities even in a very early development stage of mangrove forest, thus encouraging mangrove conservation and restoration efforts worldwide.},
}

@article {pmid36126430,
year = {2022},
author = {Mendes Dos Santos, MA and Dias, LS and Ramirez Pavon, JA and Viniski, AE and Campos Souza, CL and Pepato, MA and Correa de Azevedo, V and Teixeira Nunes, MR and Slhessarenko, RD},
title = {Regional mutations in CHIKV-ECSA genomes and detection of other viruses in the serum of acute febrile patients by a metagenomic approach in Mato Grosso, Central-Western Brazil, 2018.},
journal = {Virology},
volume = {576},
number = {},
pages = {18-29},
doi = {10.1016/j.virol.2022.08.013},
pmid = {36126430},
issn = {1096-0341},
abstract = {Mato Grosso (MT) State is part of central western Brazil and has a tropical permissive environment that favors arbovirus outbreaks. A metagenomic approach was used to identify viral genomes in seven pools of serum from patients (n=65) with acute febrile disease. Seven chikungunya virus (CHIKV) genomes were determined, showing four amino acid changes found only in CHIKV genomes obtained in MT since 2018: nsP2:T31I, nsP3: A388V, E3:T201I and E3:H57R, in addition to other mutations in E1, nsP2 and nsP4. Six parvovirus B19 (B19V) genotype I genomes (4771-5131 nt) showed four aa alterations (NS1:N473D, R579Q; VP1:I716T; and 11 kDa:V44A) compared to most similar B19V from the USA. Coinfection between CHIKV and B19V was evidenced in 22/65 (33.8%) patients by RT‒PCR and PCR, respectively. Other viruses found in these pools include human pegivirus C, torque teno virus 3, an unclassified TTV and torque teno mini virus. Metagenomics represents a useful approach to detect viruses in the serum of acute febrile patients suspected of arbovirus disease.},
}

@article {pmid36126379,
year = {2022},
author = {Roessler, J and Leistner, DM and Landmesser, U and Haghikia, A},
title = {Modulatory role of gut microbiota in cholesterol and glucose metabolism: Potential implications for atherosclerotic cardiovascular disease Atherosclerosis.},
journal = {Atherosclerosis},
volume = {359},
number = {},
pages = {1-12},
doi = {10.1016/j.atherosclerosis.2022.08.018},
pmid = {36126379},
issn = {1879-1484},
abstract = {Accumulating evidence suggests an important role of gut microbiota in physiological processes of host metabolism as well as cardiometabolic disease. Recent advances in metagenomic and metabolomic research have led to discoveries of novel pathways in which intestinal microbial metabolism of dietary nutrients is linked to metabolic profiles and cardiovascular disease risk. A number of metaorganismal circuits have been identified by microbiota transplantation studies and experimental models using germ-free rodents. Many of these pathways involve gut microbiota-related bioactive metabolites that impact host metabolism, in particular lipid and glucose homeostasis, partly via specific host receptors. In this review, we summarize the current knowledge of how the gut microbiome can impact cardiometabolic phenotypes and provide an overview of recent advances of gut microbiome research. Finally, the potential of modulating intestinal microbiota composition and/or targeting microbiota-related pathways for novel preventive and therapeutic strategies in cardiometabolic and cardiovascular diseases will be discussed.},
}

@article {pmid36125864,
year = {2022},
author = {Pallen, MJ and Rodriguez-R, LM and Alikhan, NF},
title = {Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.005482},
pmid = {36125864},
issn = {1466-5034},
abstract = {Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.},
}

@article {pmid36125772,
year = {2022},
author = {Bornemann, TLV and Adam, PS and Probst, AJ},
title = {Reconstruction of Archaeal Genomes from Short-Read Metagenomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2522},
number = {},
pages = {487-527},
pmid = {36125772},
issn = {1940-6029},
abstract = {As the majority of biological diversity remains unexplored and uncultured, investigating it requires culture-independent approaches. Archaea in particular suffer from a multitude of issues that make their culturing problematic, from them being frequently members of the rare biosphere, to low growth rates, to them thriving under very specific and often extreme environmental and community conditions that are difficult to replicate. OMICs techniques are state of the art approaches that allow direct high-throughput investigations of environmental samples at all levels from nucleic acids to proteins, lipids, and secondary metabolites. Metagenomics, as the foundation for other OMICs techniques, facilitates the identification and functional characterization of the microbial community members and can be combined with other methods to provide insights into the microbial activities, both on the RNA and protein levels. In this chapter, we provide a step-by-step workflow for the recovery of archaeal genomes from metagenomes, starting from raw short-read sequences. This workflow can be applied to recover bacterial genomes as well.},
}

@article {pmid36125771,
year = {2022},
author = {Adam, PS and Bornemann, TLV and Probst, AJ},
title = {Progress and Challenges in Studying the Ecophysiology of Archaea.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2522},
number = {},
pages = {469-486},
pmid = {36125771},
issn = {1940-6029},
abstract = {It has been less than two decades since the study of archaeal ecophysiology has become unshackled from the limitations of cultivation and amplicon sequencing through the advent of metagenomics. As a primer to the guide on producing archaeal genomes from metagenomes, we briefly summarize here how different meta'omics, imaging, and wet lab methods have contributed to progress in understanding the ecophysiology of Archaea. We then peer into the history of how our knowledge on two particularly important lineages was assembled: the anaerobic methane and alkane oxidizers, encountered primarily among Euryarchaeota, and the nanosized, mainly parasitic, members of the DPANN superphylum.},
}

@article {pmid36125585,
year = {2022},
author = {Aydin, S and Erözden, AA and Tavşanlı, N and Müdüroğlu, A and Çalışkan, M and Kara, İ},
title = {Anthocyanin Addition to Kefir: Metagenomic Analysis of Microbial Community Structure.},
journal = {Current microbiology},
volume = {79},
number = {11},
pages = {327},
pmid = {36125585},
issn = {1432-0991},
support = {38774//Istanbul Üniversitesi/ ; },
abstract = {The addition of anthocyanin to kefir for the production of more functional and bio-diversified kefir beverages has the potential to increase kefir's healthful activities. In the present study, anthocyanin extracts, obtained from black carrots, were added into kefir mixture during the fermentation process in different concentrations (1% and 5%, w/v). These kefir samples were then analyzed in terms of their microbiological qualities by metagenomic analysis. The results of the analyses show that the addition of anthocyanin has significant impacts on the community structure of kefir microbiome which in turn directly affects the expected health impacts of the beverage. Kefir with no anthocyanin included predominantly probiotic bacteria such as Lactococcus lactis (34%) and Lactobacillus kefiri (34%). On the other hand, kefir with 1% anthocyanin demonstrated a more balanced distribution of probiotic species like Lb. kefiri (17%), Leuconostoc mesenteroides (9%), and Lc. lactis (5%) at similar abundance rates. 5% anthocyanin kefir demonstrated the highest polarity in the community with a strong dominance of probiotic Lb. kefiri (72%), and distinctly less abundant bacteria such as Streptococcus salivarius subsp. thermophilus (3%). These findings provide that fortification with anthocyanins can be utilized to enhance the quality, composition, and beneficial functions of kefir.},
}

@article {pmid36125556,
year = {2022},
author = {Yang, S and Zhang, D and Zhang, Y and Fan, Z and Jiang, L and Wang, Y and Zhang, W},
title = {Multiple novel smaco-like viruses identified in chicken cloaca swabs.},
journal = {Archives of virology},
volume = {},
number = {},
pages = {},
pmid = {36125556},
issn = {1432-8798},
support = {2017YFC1200201//Key Technologies Research and Development Program/ ; BE2017693//Jiangsu Provincial Key Research and Development Program/ ; 2020CPB-C11//Chengdu Giant Panda Breeding Research Foundation/ ; ZR2019MC036//Natural Science Foundation of Shandong Province/ ; },
abstract = {Viral metagenomics has been used in numerous animal virus discoveries. Recently, an unprecedented diversity of CRESS DNA viruses was identified using this method, and this has expanded our understanding of the environmental distribution and host range of CRESS DNA viruses. In this study, using an unbiased viral metagenomics approach, we investigated the fecal virome of chickens collected from two farms of Anhui Province, China. Five novel CRESS DNA viruses were obtained and characterized. The genome of the five viruses is 2,401-2,742 bp in length, containing two ORFs in the same orientation. Phylogenetic analysis indicated that all five viruses have a closer genetic relationship to smacoviruses than to other viruses in the order Cremevirales. Pairwise comparison of Rep amino acid sequences showed that these five viruses had only low amino acid sequence identity (8.9%-30.6%) to members of the family Smacoviridae, and the sequence identity among the five smaco-like viruses and other unclassified smacovirus strains was 70.3-95.8%. These findings broaden our knowledge of the genetic diversity of CRESS DNA viruses and provide a basis for classification of unclassified smacoviruses.},
}

@article {pmid36125316,
year = {2022},
author = {Schuettenberg, A and Piña, A and Metrailer, M and Peláez-Sánchez, RG and Agudelo-Flórez, P and Lopez, JÁ and Ryle, L and Monroy, FP and Altin, JA and Ladner, JT},
title = {Highly Multiplexed Serology for Nonhuman Mammals.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0287322},
doi = {10.1128/spectrum.02873-22},
pmid = {36125316},
issn = {2165-0497},
abstract = {Emerging infectious diseases represent a serious and ongoing threat to humans. Most emerging viruses are maintained in stable relationships with other species of animals, and their emergence within the human population results from cross-species transmission. Therefore, if we want to be prepared for the next emerging virus, we need to broadly characterize the diversity and ecology of viruses currently infecting other animals (i.e., the animal virosphere). High-throughput metagenomic sequencing has accelerated the pace of virus discovery. However, molecular assays can detect only active infections and only if virus is present within the sampled fluid or tissue at the time of collection. In contrast, serological assays measure long-lived antibody responses to infections, which can be detected within the blood, regardless of the infected tissues. Therefore, serological assays can provide a complementary approach for understanding the circulation of viruses, and while serological assays have historically been limited in scope, recent advancements allow thousands to hundreds of thousands of antigens to be assessed simultaneously using <1 μL of blood (i.e., highly multiplexed serology). The application of highly multiplexed serology for the characterization of the animal virosphere is dependent on the availability of reagents that can be used to capture or label antibodies of interest. Here, we evaluate the utility of commercial immunoglobulin-binding proteins (protein A and protein G) to enable highly multiplexed serology in 25 species of nonhuman mammals, and we describe a competitive fluorescence-linked immunosorbent assay (FLISA) that can be used as an initial screen for choosing the most appropriate capture protein for a given host species. IMPORTANCE Antibodies are generated in response to infections with viruses and other pathogens, and they help protect against future exposures. Mature antibodies are long lived, are highly specific, and can bind to their protein targets with high affinity. Thus, antibodies can also provide information about an individual's history of viral exposures, which has important applications for understanding the epidemiology and etiology of disease. In recent years, there have been large advances in the available methods for broadly characterizing antibody-binding profiles, but thus far, these have been utilized primarily with human samples only. Here, we demonstrate that commercial antibody-binding reagents can facilitate modern antibody assays for a wide variety of mammalian species, and we describe an inexpensive and fast approach for choosing the best reagent for each animal species. By studying antibody-binding profiles in captive and wild animals, we can better understand the distribution and prevalence of viruses that could spill over into humans.},
}

@article {pmid36125273,
year = {2022},
author = {Uppal, S and Metz, JL and Xavier, RKM and Nepal, KK and Xu, D and Wang, G and Kwan, JC},
title = {Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics.},
journal = {mBio},
volume = {},
number = {},
pages = {e0152422},
doi = {10.1128/mbio.01524-22},
pmid = {36125273},
issn = {2150-7511},
abstract = {Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60-cell-line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a Gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed that this bacterium, here named "Candidatus Thermopylae lasonolidus," only has 88.78% 16S rRNA identity with the closest relative, Pedosphaera parvula Ellin514, indicating that it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-acyltransferase (AT) polyketide synthase (PKS) pathway. Compared with its host genome, the las BGC exhibits a significantly different GC content and pentanucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed, including the presence of three insertions, two single-nucleotide polymorphisms, and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the verrucomicrobial producer shows signs of genome reduction, its genome size is still fairly large (about 5 Mbp), and, compared to its closest free-living relative, it contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. IMPORTANCE While sponges are valuable sources of bioactive natural products, a majority of these compounds are produced in small quantities by uncultured symbionts, hampering the study and clinical development of these unique compounds. Lasonolide A (LSA), isolated from marine sponge Forcepia sp., is a cytotoxic molecule active at nanomolar concentrations, which causes premature chromosome condensation, blebbing, cell contraction, and loss of cell adhesion, indicating a novel mechanism of action and making it a potential anticancer drug lead. However, its limited supply hampers progression to clinical trials. We investigated the microbiome of Forcepia sp. using culture-independent DNA sequencing, identified genes likely responsible for LSA synthesis in an uncultured bacterium, and assembled the symbiont's genome. These insights provide future opportunities for heterologous expression and cultivation efforts that may minimize LSA's supply problem.},
}

@article {pmid36124804,
year = {2022},
author = {Pu, L and Shamir, R},
title = {3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {Supplement_2},
pages = {ii56-ii61},
doi = {10.1093/bioinformatics/btac468},
pmid = {36124804},
issn = {1367-4811},
support = {ECCB2022//United State-Israel Binational Science Foundation/ ; //United States National Science Foundation/ ; //Edmond J. Safra Center for Bioinformatics at Tel-Aviv University/ ; //Planning and Budgeting Committee/ ; //Council for Higher Education/ ; },
abstract = {MOTIVATION: Bacteriophages and plasmids usually coexist with their host bacteria in microbial communities and play important roles in microbial evolution. Accurately identifying sequence contigs as phages, plasmids and bacterial chromosomes in mixed metagenomic assemblies is critical for further unraveling their functions. Many classification tools have been developed for identifying either phages or plasmids in metagenomic assemblies. However, only two classifiers, PPR-Meta and viralVerify, were proposed to simultaneously identify phages and plasmids in mixed metagenomic assemblies. Due to the very high fraction of chromosome contigs in the assemblies, both tools achieve high precision in the classification of chromosomes but perform poorly in classifying phages and plasmids. Short contigs in these assemblies are often wrongly classified or classified as uncertain.

RESULTS: Here we present 3CAC, a new three-class classifier that improves the precision of phage and plasmid classification. 3CAC starts with an initial three-class classification generated by existing classifiers and improves the classification of short contigs and contigs with low confidence classification by using proximity in the assembly graph. Evaluation on simulated metagenomes and on real human gut microbiome samples showed that 3CAC outperformed PPR-Meta and viralVerify in both precision and recall, and increased F1-score by 10-60 percentage points.

The 3CAC software is available on https://github.com/Shamir-Lab/3CAC.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid36124775,
year = {2022},
author = {Li, T and Yin, Y},
title = {Critical assessment of pan-genomic analysis of metagenome-assembled genomes.},
journal = {Briefings in bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bib/bbac413},
pmid = {36124775},
issn = {1477-4054},
support = {2019-YIN//Nebraska Tobacco Settlement Biomedical Research Enhancement Funds/ ; 58-8042-7-089//United States Department of Agriculture/ ; R21AI171952/NH/NIH HHS/United States ; DBI-1933521//National Science Foundation/ ; },
abstract = {Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi'o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi'o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.},
}

@article {pmid36124109,
year = {2022},
author = {Fu, Y and Zhu, X and Cao, P and Shen, C and Qian, X and Miao, H and Yu, Y and Wang, H and Zhai, X},
title = {Metagenomic Next-Generation Sequencing in the Diagnosis of Infectious Fever During Myelosuppression Among Pediatric Patients with Hematological and Neoplastic Diseases.},
journal = {Infection and drug resistance},
volume = {15},
number = {},
pages = {5425-5434},
pmid = {36124109},
issn = {1178-6973},
abstract = {Purpose: To analyze the contribution of metagenomic next-generation sequencing (mNGS) in the guidance of clinical treatment and outcomes of infection during myelosuppression among children with hematological and neoplastic diseases.

Patients and Methods: The clinical data and results of mNGS assay of febrile patients suspected of infection were retrospectively collected. The characteristics of pathogenic microorganisms and clinical course of myelosuppressed children with hematological diseases were summarized.

Results: Our study included 70 patients (45 males) with a median age of 5 years (range: 0.5 to 13 y). During the study period, there were 96 events of suspected infection. According to comprehensive clinical diagnosis, 73 blood infections, 43 pneumonia and 2 urinary tract infections occurred. The positive rate of mNGS was significantly higher than that of traditional microbial detection (83.3% vs 17.7%). The main pathogens detected by mNGS were Pseudomonas aeruginosa, Acinetobacter, human herpesvirus, Candida and Aspergillus. The average duration of fever was 4.9 days and 11.6 days (P < 0.05), and the average cost of anti-infection treatment was RMB ¥28,077 and 39,898 (P < 0.05) among children received mNGS within 48 hours and more than 48 hours after the onset of infection symptoms.

Conclusion: mNGS contributes to clinical management of children with infection during myelosuppression, especially among patients with negative traditional microbial detection. Early implementation of mNGS in children with symptoms has a tendency to reduce the time of infection, fever and the cost of treatment.},
}

@article {pmid36123651,
year = {2022},
author = {Li, Q and Vehik, K and Li, C and Triplett, E and Roesch, L and Hu, YJ and Krischer, J},
title = {A robust and transformation-free joint model with matching and regularization for metagenomic trajectory and disease onset.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {661},
pmid = {36123651},
issn = {1471-2164},
support = {U24DK097771/DK/NIDDK NIH HHS/United States ; CA21765/CA/NCI NIH HHS/United States ; CA21765/CA/NCI NIH HHS/United States ; },
abstract = {BACKGROUND: To identify operational taxonomy units (OTUs) signaling disease onset in an observational study, a powerful strategy was selecting participants by matched sets and profiling temporal metagenomes, followed by trajectory analysis. Existing trajectory analyses modeled individual OTU or microbial community without adjusting for the within-community correlation and matched-set-specific latent factors.

RESULTS: We proposed a joint model with matching and regularization (JMR) to detect OTU-specific trajectory predictive of host disease status. The between- and within-matched-sets heterogeneity in OTU relative abundance and disease risk were modeled by nested random effects. The inherent negative correlation in microbiota composition was adjusted by incorporating and regularizing the top-correlated taxa as longitudinal covariate, pre-selected by Bray-Curtis distance and elastic net regression. We designed a simulation pipeline to generate true biomarkers for disease onset and the pseudo biomarkers caused by compositionality. We demonstrated that JMR effectively controlled the false discovery and pseudo biomarkers in a simulation study generating temporal high-dimensional metagenomic counts with random intercept or slope. Application of the competing methods in the simulated data and the TEDDY cohort showed that JMR outperformed the other methods and identified important taxa in infants' fecal samples with dynamics preceding host disease status.

CONCLUSION: Our method JMR is a robust framework that models taxon-specific trajectory and host disease status for matched participants without transformation of relative abundance, improving the power of detecting disease-associated microbial features in certain scenarios. JMR is available in R package mtradeR at https://github.com/qianli10000/mtradeR.},
}

@article {pmid36123522,
year = {2022},
author = {Ayala-Muñoz, D and Macalady, JL and Sánchez-España, J and Falagán, C and Couradeau, E and Burgos, WD},
title = {Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {36123522},
issn = {1751-7370},
abstract = {Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline. The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes. Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria. Activity for dissimilatory nitrogen cycling including nitrogen fixation and nitrate reduction was primarily predicted in the chemocline. Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer. Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in the chemocline. In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation. Based on this information we evaluated the potential for sulfide mineral precipitation in the deep layer as a tool for remediation. We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation. Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals.},
}

@article {pmid36123442,
year = {2022},
author = {Hedlund, BP and Chuvochina, M and Hugenholtz, P and Konstantinidis, KT and Murray, AE and Palmer, M and Parks, DH and Probst, AJ and Reysenbach, AL and Rodriguez-R, LM and Rossello-Mora, R and Sutcliffe, IC and Venter, SN and Whitman, WB},
title = {SeqCode: a nomenclatural code for prokaryotes described from sequence data.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {36123442},
issn = {2058-5276},
abstract = {Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.},
}

@article {pmid36123347,
year = {2022},
author = {Wu, R and Smith, CA and Buchko, GW and Blaby, IK and Paez-Espino, D and Kyrpides, NC and Yoshikuni, Y and McDermott, JE and Hofmockel, KS and Cort, JR and Jansson, JK},
title = {Structural characterization of a soil viral auxiliary metabolic gene product - a functional chitosanase.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {5485},
pmid = {36123347},
issn = {2041-1723},
support = {5 P41 RR001209//U.S. Department of Health & Human Services | NIH | National Center for Research Resources (NCRR)/ ; },
abstract = {Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin - a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.},
}

@article {pmid36123315,
year = {2022},
author = {Fontanta, F and Alessandri, G and Tarracchini, C and Bianchi, MG and Rizzo, SM and Mancabelli, L and Lugli, GA and Argentini, C and Vergna, L and Anzalone, R and Longhi, G and Viappiani, A and Taurino, G and Chiu, M and Turroni, F and Bussolati, O and van Sinderen, D and Milani, C and Ventura, M},
title = {Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16205},
pmid = {36123315},
issn = {1462-2920},
abstract = {The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant fecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings.},
}

@article {pmid36123312,
year = {2022},
author = {Perez-Molphe-Montoya, E and Küsel, K and Overholt, WA},
title = {Redefining the phylogenetic and metabolic diversity of phylum Omnitrophota.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16170},
pmid = {36123312},
issn = {1462-2920},
support = {SFB 1076//German Research Foundation/ ; CRC AquaDiva - SFB1076 - 218627073//Deutsche Forschungsgemeinschaft/ ; //Friedrich Schiller University Jena/ ; //Leibniz Institute on Aging - Fritz Lipmann Institute/ ; },
abstract = {The candidate phylum Omnitrophica-recently termed Omnitrophota, and originally known as OP3-is an understudied bacterial clade that has primarily been found in aquatic ecosystems. To characterize the diversity and ecology of this phylum, we reconstructed 55 Omnitrophota metagenome-assembled genomes (MAGs) from a well-characterized groundwater system within central Germany and placed them within the context of publicly available genomes. Seven clades were identified, four of which contained novel genomes obtained from our groundwater system. All clades exhibited the capacity for type IV pili, type II secretion systems, glycogen storage, and carbohydrate degradation. Only the characterized Cand. Omnitrophus magneticus genome exhibited functions associated with magnetosome construction. Clades were characterized by sets of traits rather than unique pathways, which were then used to infer ecological strategies. These lifestyles consisted of mixotrophs, obligate fermenters, and versatile respiratory heterotrophs. Patterns in 16S rRNA gene amplicons from a 6 years, monthly sampled groundwater time-series dataset reflected the persistent and widespread occurrence of Clade 7 Wood-Ljungdahl utilizing mixotrophs and highlight this group as a core member of the groundwater community. Overall, this study uncovered, characterized, and contextualized the metabolic and phylogenetic diversity within phylum Omnitrophota, and predicts that environmental populations may mediate both nitrogen and sulfur cycling, along with organic matter production and degradation within aquatic ecosystems.},
}

@article {pmid36122838,
year = {2022},
author = {Thompson, DS and Fu, C and Gandhi, T and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Hadden, JK and Carlson, M and Coarfa, C and Madan, A},
title = {Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients.},
journal = {Progress in neuro-psychopharmacology & biological psychiatry},
volume = {},
number = {},
pages = {110638},
doi = {10.1016/j.pnpbp.2022.110638},
pmid = {36122838},
issn = {1878-4216},
abstract = {BACKGROUND: Comorbid anxiety and depression are common and are associated with greater disease burden than either alone. Our recent efforts have identified an association between gut microbiota dysfunction and severity of anxiety and depression. In this follow-up, we applied Differential Co-Expression Analysis (DiffCoEx) to identify potential gut microbiota biomarker(s) candidates of treatment resistance among psychiatric inpatients.

METHODS: In a sample of convenience, 100 psychiatric inpatients provided clinical data at admission and discharge; fecal samples were collected early during the hospitalization. Whole genome shotgun sequencing methods were used to process samples. DiffCoEx was used to identify clusters of microbial features significantly different based on treatment resistance status. Once overlapping features were identified, a knowledge-mining tool was used to review the literature using a list of microbial species/pathways and a select number of medical subject headlines (MeSH) terms relevant for depression, anxiety, and brain-gut-axis dysregulation. Network analysis used overlapping features to identify microbial interactions that could impact treatment resistance.

RESULTS: DiffCoEx analyzed 10,403 bacterial features: 43/44 microbial features associated with depression treatment resistance overlapped with 43/114 microbial features associated with anxiety treatment resistance. Network analysis resulted in 8 biological interactions between 16 bacterial species. Clostridium perfringens evidenced the highest connection strength (0.95). Erysipelotrichaceae bacterium 6_1_45 has been most widely examined, is associated with inflammation and dysbiosis, but has not been associated with depression or anxiety.

CONCLUSION: DiffCoEx potentially identified gut bacteria biomarker candidates of depression and anxiety treatment-resistance. Future efforts in psychiatric microbiology should examine the mechanistic relationship of identified pro-inflammatory species, potentially contributing to a biomarker-based algorithm for treatment resistance.},
}

@article {pmid36121926,
year = {2022},
author = {Carratto, TMT and Moraes, VMS and Recalde, TSF and Oliveira, MLG and Teixeira Mendes-Junior, C},
title = {Applications of massively parallel sequencing in forensic genetics.},
journal = {Genetics and molecular biology},
volume = {45},
number = {3 Suppl 1},
pages = {e20220077},
doi = {10.1590/1678-4685-GMB-2022-0077},
pmid = {36121926},
issn = {1415-4757},
abstract = {Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.},
}

@article {pmid36121483,
year = {2022},
author = {Gill, SP and Hunter, WR and Coulson, LE and Banat, IM and Schelker, J},
title = {Synthetic and biological surfactant effects on freshwater biofilm community composition and metabolic activity.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {36121483},
issn = {1432-0614},
abstract = {Surfactants are used to control microbial biofilms in industrial and medical settings. Their known toxicity on aquatic biota, and their longevity in the environment, has encouraged research on biodegradable alternatives such as rhamnolipids. While previous research has investigated the effects of biological surfactants on single species biofilms, there remains a lack of information regarding the effects of synthetic and biological surfactants in freshwater ecosystems. We conducted a mesocosm experiment to test how the surfactant sodium dodecyl sulfate (SDS) and the biological surfactant rhamnolipid altered community composition and metabolic activity of freshwater biofilms. Biofilms were cultured in the flumes using lake water from Lake Lunz in Austria, under high (300 ppm) and low (150 ppm) concentrations of either surfactant over a four-week period. Our results show that both surfactants significantly affected microbial diversity. Up to 36% of microbial operational taxonomic units were lost after surfactant exposure. Rhamnolipid exposure also increased the production of the extracellular enzymes, leucine aminopeptidase, and glucosidase, while SDS exposure reduced leucine aminopeptidase and glucosidase. This study demonstrates that exposure of freshwater biofilms to chemical and biological surfactants caused a reduction of microbial diversity and changes in biofilm metabolism, exemplified by shifts in extracellular enzyme activities. KEY POINTS: • Microbial biofilm diversity decreased significantly after surfactant exposure. • Exposure to either surfactant altered extracellular enzyme activity. • Overall metabolic activity was not altered, suggesting functional redundancy.},
}

@article {pmid36121227,
year = {2022},
author = {Ramos-Tapia, I and Nuñez, R and Salinas, C and Salinas, P and Soto, J and Paneque, M},
title = {Study of Wetland Soils of the Salar de Atacama with Different Azonal Vegetative Formations Reveals Changes in the Microbiota Associated with Hygrophile Plant Type on the Soil Surface.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0053322},
doi = {10.1128/spectrum.00533-22},
pmid = {36121227},
issn = {2165-0497},
abstract = {Salar de Atacama is located approximately 55 km south of San Pedro de Atacama in the Antofagasta region, Chile. The high UV irradiation and salt concentration and extreme drought make Salar de Atacama an ideal site to search for novel soil microorganisms with unique properties. Here, we used a metataxonomic approach (16S rRNA V3-V4) to identify and characterize the soil microbiota associated with different surface azonal vegetation formations, including strict hygrophiles (Baccharis juncea, Juncus balticus, and Schoenoplectus americanus), transitional hygrophiles (Distichlis spicata, Lycium humile, and Tessaria absinthioides), and their various combinations. We detected compositional differences among the soil surface microbiota associated with each plant formation in the sampling area. There were changes in soil microbial phylogenetic diversity from the strict to the transitional hygrophiles. Moreover, we found alterations in the abundance of bacterial phyla and genera. Halobacteriota and Actinobacteriota might have facilitated water uptake by the transitional hygrophiles. Our findings helped to elucidate the microbiota of Salar de Atacama and associate them with the strict and transitional hygrophiles indigenous to the region. These findings could be highly relevant to future research on the symbiotic relationships between microbiota and salt-tolerant plants in the face of climate change-induced desertification. IMPORTANCE The study of the composition and diversity of the wetland soil microbiota associated with hygrophilous plants in a desert ecosystem of the high Puna in northern Chile makes it an ideal approach to search for novel extremophilic microorganisms with unique properties. These microorganisms are adapted to survive in ecological niches, such as those with high UV irradiation, extreme drought, and high salt concentration; they can be applied in various fields, such as biotechnology and astrobiology, and industries, including the pharmaceutical, food, agricultural, biofuel, cosmetic, and textile industries. These microorganisms can also be used for ecological conservation and restoration. Extreme ecosystems are a unique biological resource and biodiversity hot spots that play a crucial role in maintaining environmental sustainability. The findings could be highly relevant to future research on the symbiotic relationships between microbiota and extreme-environment-tolerant plants in the face of climate change-induced desertification.},
}

@article {pmid36121163,
year = {2022},
author = {Fierer, N and Holland-Moritz, H and Alexiev, A and Batther, H and Dragone, NB and Friar, L and Gebert, MJ and Gering, S and Henley, JB and Jech, S and Kibby, EM and Melie, T and Patterson, WB and Peterson, E and Schutz, K and Stallard-Olivera, E and Sterrett, J and Walsh, C and Mansfeldt, C},
title = {A Metagenomic Investigation of Spatial and Temporal Changes in Sewage Microbiomes across a University Campus.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0065122},
doi = {10.1128/msystems.00651-22},
pmid = {36121163},
issn = {2379-5077},
abstract = {Wastewater microbial communities are not static and can vary significantly across time and space, but this variation and the factors driving the observed spatiotemporal variation often remain undetermined. We used a shotgun metagenomic approach to investigate changes in wastewater microbial communities across 17 locations in a sewer network, with samples collected from each location over a 3-week period. Fecal material-derived bacteria constituted a relatively small fraction of the taxa found in the collected samples, highlighting the importance of environmental sources to the sewage microbiome. The prokaryotic communities were highly variable in composition depending on the location within the sampling network, and this spatial variation was most strongly associated with location-specific differences in sewage pH. However, we also observed substantial temporal variation in the composition of the prokaryotic communities at individual locations. This temporal variation was asynchronous across sampling locations, emphasizing the importance of independently considering both spatial and temporal variation when assessing the wastewater microbiome. The spatiotemporal patterns in viral community composition closely tracked those of the prokaryotic communities, allowing us to putatively identify the bacterial hosts of some of the dominant viruses in these systems. Finally, we found that antibiotic resistance gene profiles also exhibit a high degree of spatiotemporal variability, with most of these genes unlikely to be derived from fecal bacteria. Together, these results emphasize the dynamic nature of the wastewater microbiome, the challenges associated with studying these systems, and the utility of metagenomic approaches for building a multifaceted understanding of these microbial communities and their functional attributes. IMPORTANCE Sewage systems harbor extensive microbial diversity, including microbes derived from both human and environmental sources. Studies of the sewage microbiome are useful for monitoring public health and the health of our infrastructure, but the sewage microbiome can be highly variable in ways that are often unresolved. We sequenced DNA recovered from wastewater samples collected over a 3-week period at 17 locations in a single sewer system to determine how these communities vary across time and space. Most of the wastewater bacteria, and the antibiotic resistance genes they harbor, were not derived from human feces, but human usage patterns did impact how the amounts and types of bacteria and bacterial genes we found in these systems varied over time. Likewise, the wastewater communities, including both bacteria and their viruses, varied depending on location within the sewage network, highlighting the challenges and opportunities in efforts to monitor and understand the sewage microbiome.},
}

@article {pmid36121162,
year = {2022},
author = {Bulzu, PA and Kavagutti, VS and Andrei, AS and Ghai, R},
title = {The Evolutionary Kaleidoscope of Rhodopsins.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0040522},
doi = {10.1128/msystems.00405-22},
pmid = {36121162},
issn = {2379-5077},
abstract = {Rhodopsins are widely distributed across all domains of life where they perform a plethora of functions through the conversion of electromagnetic radiation into physicochemical signals. As a result of an extensive survey of available genomic and metagenomic sequencing data, we reported the existence of novel clades and exotic sequence motifs scattered throughout the evolutionary radiations of both Type-1 and Type-3 rhodopsins that will likely enlarge the optogenetics toolbox. We expanded the typical rhodopsin blueprint by showing that a highly conserved and functionally important arginine residue (i.e., Arg82) was substituted multiple times during evolution by an extensive amino acid spectrum. We proposed the umbrella term Alt-rhodopsins (AltRs) for all such proteins that departed Arg82 orthodoxy. Some AltRs formed novel clades in the rhodopsin phylogeny and were found in giant viruses. Some newly uncovered AltRs were phylogenetically close to heliorhodopsins, which allowed a closer examination of the phylogenetic border between Type-1 rhodopsins and heliorhodopsins. Comprehensive phylogenetic trees and ancestral sequence reconstructions allowed us to advance the hypothesis that proto-heliorhodopsins were a eukaryotic innovation before their subsequent diversification into the extant Type-3 rhodopsins. IMPORTANCE The rhodopsin scaffold is remarkably versatile and widespread, coupling light availability to energy production and other light-dependent cellular responses with minor alterations to critical residues. We described an unprecedented spectrum of substitutions at one of the most conserved amino acids in the rhodopsin fold, Arg82. We denoted such phylogenetically diverse rhodopsins with the umbrella name Alt-rhodopsins (AltR) and described a distinct branch of AltRs in giant viruses. Intriguingly, some AltRs were the closest phylogenetic neighbors to Heliorhodopsins (HeRs) whose origins have remained enigmatic. Our analyses of HeR origins in the light of AltRs led us to posit a most unusual evolutionary trajectory that suggested a eukaryotic origin for HeRs before their diversification in prokaryotes.},
}

@article {pmid36121066,
year = {2022},
author = {Shi, T and Zhang, T and Wang, X and Wang, X and Shen, W and Guo, X and Liu, Y and Li, Z and Jiang, Y},
title = {Metagenomic Analysis of in Vitro Ruminal Fermentation Reveals the Role of the Copresent Microbiome in Plant Biomass Degradation.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.2c03522},
pmid = {36121066},
issn = {1520-5118},
abstract = {In vitro ruminal fermentation is considered an efficient way to degrade crop residue. To better understand the microbial communities and their functions during in vitro ruminal fermentation, the microbiome and short chain fatty acid (SCFA) production were investigated using the metagenomic sequencing and rumen simulation technique (RUSITEC) system. A total of 1677 metagenome-assembled genomes (MAGs) were reconstructed, and 298 MAGs were found copresenting in metagenomic data of the current work and 58 previously ruminal representative samples. Additionally, the domains related to pectin and xylan degradation were overrepresented in the copresent MAGs compared with total MAGs. Among the copresent MAGs, we obtained 14 MAGs with SCFA-synthesis-related genes positively correlated with SCFA concentrations. The MAGs obtained from this study enable a better understanding of dominant microbial communities across in vivo and in vitro ruminal fermentation and show promise for pointing out directions for further research on in vitro ruminal fermentation.},
}

@article {pmid36120548,
year = {2022},
author = {Lee, J and Um, S and Kim, SH},
title = {Metabolomic analysis of halotolerant endophytic bacterium Salinivibrio costicola isolated from Suaeda maritima (L.) dumort.},
journal = {Frontiers in molecular biosciences},
volume = {9},
number = {},
pages = {967945},
pmid = {36120548},
issn = {2296-889X},
abstract = {In this study, the Salinivibrio costicola strain was isolated from Suaeda maritima (L.) Dumort. collected in Sinan, Republic of Korea. The endophytic characteristics of the Gram-negative bacterium S. costicola were verified with metagenomics sequencing of S. maritima. S. costicola was cultivated for 3 days in a liquid medium with 3.3% sea salt and analyzed the metabolites produced by the strain cultured in five different bacterial cultivation media. From the bacterial cultures, polyhydroxybutyrate derivatives were detected using high-resolution mass spectrometry, and three major compounds were isolated by high-performance liquid chromatography. The chemical structures of the compounds were elucidated using nuclear magnetic resonance and MS analyses. The relationship between the compounds was confirmed with Global Natural Product Social Molecular Networking, which showed clustering of the compounds. From the S. maritima extract, polyhydroxybutyrate derivatives produced by S. costicola were detected as being accumulated in the host plant.},
}

@article {pmid36120127,
year = {2022},
author = {Cao, P and Wei, X and Wang, G and Chen, X and Han, J and Li, Y},
title = {Microbial inoculants and garbage fermentation liquid reduced root-knot nematode disease and As uptake in Panax quinquefolium cultivation by modulating rhizosphere microbiota community.},
journal = {Chinese herbal medicines},
volume = {14},
number = {1},
pages = {58-69},
pmid = {36120127},
issn = {2589-3610},
abstract = {Objective: To find a suitable ecological cultivation measure to solve the problem of root-knot nematode disease of Panax quinquefolium (Panacis Quinquefolii Radix) and the heavy metals accumulating in its roots.

Methods: Three-year-old P. quinquefolium was treated with four different combinations of microbial inoculant (MI) and garbage fermentation liquid (GFL) [the joint application of 'TuXiu' MI and Fifty potassium MI (TF), the combination use of 'No. 1' MI and Fifty potassium MI (NF), 'Gulefeng' poly-γ-glutamic acid MI (PGA), GFL], and the untreated control (CK). Here, high-throughput sequencing, ICP-MS and UPLC were employed to systematically characterize changes of microbial diversity and structure composition, heavy metals (As, Cd and Pb) content and ginsenoside content among different treatments.

Results: The results revealed that different MIs and GFL could increase the root dry weight of P. quinquefolium, PGA enhanced it by 83.24%, followed by GFL (49.93%), meanwhile, PGA and GFL were able to lessen root-knot nematode disease incidence by 57.25% and 64.35%. The treatment of PGA and GFL can also effectively reduce heavy metals in roots. The As content in GFL and PGA was decreased by 52.17% and 43.48% respectively, while the Cd and Pb contents of GFL and PGA was decreased somewhat. Additionally, the content of total ginsenosides was increased by 42.14% and 42.07%, in response to TF and NF, respectively. Our metagenomic analysis showed that the relative abundance of particular soil microbial community members related to the biocontrol of root-knot nematode disease and plant pathogen (i.e., Chaetomium in NF, Xylari in GFL, and Microascus in PGA), heavy metal bioremediation (Hyphomacrobium in PGA and Xylaria in GFL), and nitrogen fixation (Nordella and Nitrospira in TF) was significantly increased; notably, potential harmful microflora, such as Plectosaphaerella and Rhizobacter, were more abundant in the control group.

Conclusion: MI and GFL could improve the quality of P. quinquefolium by modifying its rhizosphere microbial community structure and composition, both of them are beneficial to the development of ecological cultivation of P. quinquefolium.},
}

@article {pmid36119925,
year = {2022},
author = {Prasetiyono, BWHE and Widiyanto, W and Pandupuspitasari, NS},
title = {Gut Microbiota Profiles in Dairy Cattle from Highland and Coastal Regions Using Shotgun Metagenomic Approach.},
journal = {BioMed research international},
volume = {2022},
number = {},
pages = {3659052},
pmid = {36119925},
issn = {2314-6141},
mesh = {Animals ; Cattle ; Firmicutes ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {There is significant difference in milk production of highland and coastal regions in Indonesia of which the latter is critically low. The recent studies indicate a possibility of improving the milk yield and quality by manipulating the gut microbiota, for which profiling and abundance of gut microbiota in these divergent regions need to be addressed. The present study was the first of its kind to explore the dairy cattle gut microbiota diversity, abundance, and functional annotation of the two divergent Indonesian regions, the highland and coastal regions, by shotgun metagenomic approach. Unfavorable environmental conditions such as type of forage grass in coastal regions and high temperature remain a limiting factor; however, the improvement through manipulating the gut microbiota was not considered until recently to improve the quality and quantity of coastal region dairy cattle. The application of recent advance technologies can help achieve this goal on sustainable basis. The results show Bacteroidetes in higher abundance in coastal region (FPP) than in highland (Salatiga) while Firmicutes were higher in Salatiga. Furthermore, a collective physiology of the community was found by annotating the sequences against KEGG, eggNOG, and CAZy databases. To identify the role in pathways, an mPATH analysis was performed to have insight into the microbiota community in different metabolic pathways. The identified targets can be used as prebiotic and/or probiotic to improve the average milk yield of coastal region dairy cattle by manipulating the dairy feed with desired microbes.},
}

Animals
Cattle
Firmicutes
*Gastrointestinal Microbiome/genetics
Metagenome
Metagenomics
*Microbiota

@article {pmid36119702,
year = {2022},
author = {Wang, L and Wang, F and Yang, C and Luo, F},
title = {Central nervous system infection caused by Mycobacterium houstonense: A case report.},
journal = {Frontiers in neurology},
volume = {13},
number = {},
pages = {908086},
pmid = {36119702},
issn = {1664-2295},
abstract = {Background: Mycobacterium houstonense is a rapidly growing mycobacterium (RGM) that belongs to the unnamed third biovariant complex of the Mycobacterium fortuitum group, which is rarely responsible for human infection. Approximately 76% of infections caused by the M. fortuitum group occur after open fractures or skin, soft tissue, bone, or puncture wounds. To date, only a few cases of human infectious disease caused by M. houstonense have been reported worldwide.

Case presentation: We present a case of a 26-year-old man with a central nervous system (CNS) infection caused by M. houstonense. The patient was transferred to our hospital because of headaches and muscle strength changes. One month prior to presentation at our hospital, the patient was diagnosed with tuberculous meningitis at the other two hospitals, but his condition did not improve after anti-tuberculous treatment, antibiotics, and anti-viral treatment before admission to our hospital. Lumbar puncture was performed at both previous hospitals, as well as at our hospital; the results consistently indicated high cerebrospinal fluid (CSF) opening pressure. M. houstonense was detected in the CSF of the second hospital's lumbar puncture by metagenomic next-generation sequencing (mNGS) but was not identified at our hospital. The patient was discharged from our hospital after receiving non-tuberculous mycobacterium (NTM) treatment for 1 month according to the Chinese NTM guidelines. However, the patient died 20 days after discharge.

Conclusion: Since it is difficult to identify M. houstonense, this is the first case of human CNS infection caused by M. houstonense in China. This case may be considered by neurologists and infectious physicians when CNS infection does not respond to conventional treatment, especially in the uncommon type of NTM.},
}

@article {pmid36119002,
year = {2020},
author = {Xu, LL and Ling, XF and Zhao, SJ and Wang, RF and Wang, ZT},
title = {Distribution and diversity of endophytic fungi in Gentiana rigescens and cytotoxic activities.},
journal = {Chinese herbal medicines},
volume = {12},
number = {3},
pages = {297-302},
pmid = {36119002},
issn = {2589-3610},
abstract = {Objective: In the present study, Gentiana rigescens was screened for fungi communities to clarify their diversity and community assemblage in hosts. Meanwhile, the identification and activity assays of the strains were also conducted.

Methods: By culture-dependent (endophytic fungi isolations from plant sections) and culture-independent (metagenomic library and cloning from plant sections) techniques, fungi communities were studied. The metagenomic library was generated using direct DNA isolation of whole plants, plant radixes, plant stems, plant leaves, plant flowers and soils around the plant. Meanwhile, endophytes were isolated from all parts of G. rigescens plants. After fermentation of the fungi isolations, all the isolates were evaluated for their cytotoxicity against four kinds of human cancer cell lines (HCT116, BEL7404, A549, MDA-MB-231).

Results: Eventually, 200 strains were isolated and 103 strains were further identified through the internal transcribed spacer (ITS, ITS1 and ITS2 regions) sequence by using the universal primers ITS5 and ITS4. A total of 59,106 fungal sequences corresponding to 374 putative operational taxonomic units (OTU) were identified by 454 pyrosequencing. Through 454 pyrosequencing, the main fungal genera were Sebacina, Botrytis, Mycosphaerella, Boletus and Gibberella, and the major fungal genera which were directly isolated were Aspergillus, Fusarium, Penicillium and Alternaria. Activity assays showed strains 5-26 (Aspergillus sp.) and 6-2 (Fusarium avenaceum) had the outstanding cytotoxicity to all the tested cell lines with IC50 values <5 μg/mL.

Conclusion: This study revealed the abundance of endogenetic fungal resources and a variety of genetic information in G. rigescens by high-throughput 454 sequencing technology and fungi isolation methods. Activity assays indicated that endophytes were a promising natural source of potential anticancer agents.},
}

@article {pmid36118848,
year = {2022},
author = {Rabapane, KJ and Ijoma, GN and Matambo, TS},
title = {Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {946449},
pmid = {36118848},
issn = {1664-8021},
abstract = {Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.},
}

@article {pmid36118360,
year = {2022},
author = {Liu, Z and Ding, X and Haider, MS and Ali, F and Yu, H and Chen, X and Tan, S and Zu, Y and Liu, W and Ding, B and Zheng, A and Zheng, J and Qian, Z and Ashfaq, H and Yu, D and Li, K},
title = {A metagenomic insight into the Yangtze finless porpoise virome.},
journal = {Frontiers in veterinary science},
volume = {9},
number = {},
pages = {922623},
pmid = {36118360},
issn = {2297-1769},
abstract = {The Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) inhabiting the Yantze River, China is critically endangered because of the influences of infectious disease, human activity, and water contamination. Viral diseases are one of the crucial factors that threatening the health of Yangtze finless porpoise. However, there are few studies which elaborate the viral diversity of Yangtze finless. Therefore, this study was performed to investigate the viral diversity of Yangtze finless by metagenomics. Results indicated that a total of 12,686,252 high-quality valid sequences were acquired and 2,172 virus reads were recognized. Additionally, we also obtained a total of 10,600 contigs. Phages was the most abundant virus in the samples and the ratio of DNA and RNA viruses were 69.75 and 30.25%, respectively. Arenaviridae, Ackermannviridae and Siphoviridae were the three most predominant families in all the samples. Moreover, the majority of viral genus were Mammarenavirus, Limestonevirus and Lambdavirus. The results of gene prediction indicated that these viruses play vital roles in biological process, cellular component, molecular function, and disease. To the best of our knowledge, this is the first report on the viral diversity of Yangtze finless porpoise, which filled the gaps in its viral information. Meanwhile, this study can also provide a theoretical basis for the establishment of the prevention and protection system for virus disease of Yangtze finless porpoise.},
}

@article {pmid36118221,
year = {2022},
author = {Gu, X and Zhao, L and Tan, J and Zhang, Q and Fu, L and Li, J},
title = {Characterization of a novel β-agarase from Antarctic macroalgae-associated bacteria metagenomic library and anti-inflammatory activity of the enzymatic hydrolysates.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {972272},
pmid = {36118221},
issn = {1664-302X},
abstract = {An agarase gene (aga1904) that codes a protein with 640 amino acids was obtained from the metagenomic library of macroalgae-associated bacteria collected from King George Island, Antarctica. Gene aga1904 was expressed in Escherichia coli BL21 (DE3) and recombinant Aga1904 was purified by His Bind Purification kit. The optimal temperature and pH for the activity of Aga1904 were 50°C and 6.0, respectively. Fe3+ and Cu2+ significantly inhibited the activity of Aga1904. The V max and K m values of recombinant Aga1904 were 108.70 mg/ml min and 6.51 mg/ml, respectively. The degradation products of Aga1904 against agarose substrate were mainly neoagarobiose, neoagarotetraose, and neoagarohexaose analyzed by thin layer chromatography. The cellular immunoassay of enzymatic hydrolysates was subsequently carried out, and the results showed that agaro-oligosaccharides dominated by neoagarobiose significantly inhibited key pro-inflammatory markers including, nitric oxide (NO), interleukins 6 (IL-6), and tumor necrosis factor α (TNF-α). This work provides a promising candidate for development recombinant industrial enzyme to prepare agaro-oligosaccharides, and paved up a new path for the exploitation of natural anti-inflammatory agent in the future.},
}

@article {pmid36118217,
year = {2022},
author = {Achee, NL and , },
title = {The Remote Emerging Disease Intelligence-NETwork.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {961065},
pmid = {36118217},
issn = {1664-302X},
abstract = {Accurate prediction of zoonotic spillover events requires a detailed understanding of baseline pathogens circulating in differing global environments. By characterizing the diversity and determining the natural baseline of pathogens in a given biological system, any perturbations to this balance can be detected, leading to estimates of risk for emerging diseases. As epidemics and probability for pandemics increase, there is a fundamental need for building global collaborations to fill gaps in the surveillance effort, especially to build remote in-county capacity and standardize timely sample processing and data analysis. To this point, a new consortium, the Remote Emerging Disease Intelligence-NETwork (REDI-NET) has been established to enhance surveillance approaches and characterize natural pathogens in temperate, tropical forest, and tropical grassland biomes. The REDI-NET is envisioned to be a long-term, phased initiative. All phases will integrate accompanying training resources such as videos reflecting SOPs and Quick Reference Guides. Routine bio- and xenosurveillance will facilitate the characterization of ecological parameters, enhance the accuracy of vector species identification using artificial intelligence technology, and guide the establishment of epidemiological risk thresholds critical for mitigating disease outbreaks in a timely manner. A key deliverable of the REDI-NET is a custom-designed electronically merged (e-MERGE) data pipeline and alert dashboard that integrates remotely captured data with state-of-the-art metagenomic next-generation sequencing technology. This pipeline incorporates data generated from field and laboratory best practices, to furnish health decision-makers with a centralized, timely, and rigorous database to efficiently search interdisciplinary and heterogeneous data sources necessary to alert, prepare and mitigate health threats. The e-MERGE pipeline, once fully established, will be a flexible, scalable, and expandable tool for varied health applications. Program success will result in an operational framework that addresses resource gaps in pathogen surveillance and enhances health protection with broad global applicability. The objective of this manuscript is to introduce the REDI-NET framework to anticipated stakeholders engaged in metagenomics, epidemiological surveillance, and One Health with a focus on Phase 1.},
}