@article {pmid36996924, year = {2023}, author = {Wang, X and Chen, D and Zhou, Y and Yu, M and Niu, J}, title = {Degradation performance and potential protection mechanism of the anammox consortia in response to capecitabine.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {138539}, doi = {10.1016/j.chemosphere.2023.138539}, pmid = {36996924}, issn = {1879-1298}, abstract = {The potential risks of anti-cancer drugs such as capecitabine have attracted considerable attention due to their continuous release. Understanding the response of removal performance and protective mechanism to the presence of emerging contaminants is crucial for the application of anammox techniques in wastewater treatment. Capecitabine affected the nitrogen removal performance slightly in the activity experiment. Due to bio-adsorption and biodegradation, up to 64-70% of the capecitabine can be removed effectively. However, 10 mg/L of capecitabine significantly decreased the removal efficiency of capecitabine and total nitrogen at repeated load of capecitabine. Metabolomic analysis revealed the metabolites 5'-deoxy-5-fluorocytidine and alpha-fluoro-beta-alanine, while metagenomic analysis confirmed the biodegradation pathway and underlying gene distribution. The potentially protective mechanisms of the system against capecitabine were the increased heterotrophic bacteria and secretion of sialic acid. Blast analysis confirmed the presence of potential genes involved in the complete biosynthesis pathway of sialic acid in anammox bacteria, some of which are also found in Nitrosomonas, Thauera, and Candidatus Promineofilum.}, }
@article {pmid36996871, year = {2023}, author = {Servellita, V and Gonzalez, AS and Lamson, DM and Foresythe, A and Huh, HJ and Bazinet, AL and Bergman, NH and Bull, RL and Garcia, KY and Goodrich, JS and Lovett, SP and Parker, K and Radune, D and Hatada, A and Pan, CY and Rizzo, K and Bertumen, JB and Morales, C and Oluniyi, PE and Nguyen, J and Tan, J and Stryke, D and Jaber, R and Leslie, MT and Lyons, Z and Hedman, HD and Parashar, U and Sullivan, M and Wroblewski, K and Oberste, MS and Tate, JE and Baker, JM and Sugerman, D and Potts, C and Lu, X and Chhabra, P and ,  and Ingram, LA and Shiau, H and Britt, W and Sanchez, LHG and Ciric, C and Rostad, CA and Vinjé, J and Kirking, HL and Wadford, DA and Raborn, RT and St George, K and Chiu, CY}, title = {Adeno-associated virus type 2 in US children with acute severe hepatitis.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-023-05949-1}, pmid = {36996871}, issn = {1476-4687}, abstract = {As of August 2022, clusters of acute severe hepatitis of unknown etiology in children have been reported from 35 countries, including the United States[1,2]. Previous studies have found human adenoviruses (HAdVs) in the blood from cases in Europe and the United States[3-7], although it is unclear whether this virus is causative. Here we used PCR testing, viral enrichment based sequencing, and agnostic metagenomic sequencing to analyze samples from 16 HAdV-positive cases from October 1, 2021 to May 22, 2022, in parallel with 113 controls. In blood from 14 cases, adeno-associated virus 2 (AAV2) sequences were detected in 93% (13 of 14), compared to 4 (3.5%) of 113 controls (P<0.001) and to 0 of 30 patients with hepatitis of defined etiology (P<0.001). In controls, HAdV-41 was detected in blood from 9 (39.1%) of the 23 patients with acute gastroenteritis (without hepatitis), including 8 of 9 patients with positive stool HAdV testing, but co-infection with AAV2 was observed in only 3 (13.0%) of these 23 patients versus 93% of cases (P<0.001). Co-infections by Epstein-Barr virus (EBV), human herpesvirus 6 (HHV-6), and/or enterovirus A71 (EV-A71) were also detected in 12 (85.7%) of 14 cases, with higher herpesvirus detection in cases versus controls (P<0.001). Our findings suggest that the severity of the disease is related to co-infections involving AAV2 and one or more helper viruses.}, }
@article {pmid36996751, year = {2023}, author = {Yin, X and Li, L and Chen, X and Liu, YY and Lam, TT and Topp, E and Zhang, T}, title = {Global environmental resistome: Distinction and connectivity across diverse habitats benchmarked by metagenomic analyses.}, journal = {Water research}, volume = {235}, number = {}, pages = {119875}, doi = {10.1016/j.watres.2023.119875}, pmid = {36996751}, issn = {1879-2448}, abstract = {The widely distributed antibiotic resistance genes (ARGs) were unevenly proliferated in various habitats. Great endeavors are needed to resolve the resistome features that can differentiate or connect different habitats. This study retrieved a broad spectrum of resistome profiles from 1723 metagenomes categorized into 13 habitats, encompassing industrial, urban, agricultural, and natural environments, and spanning most continents and oceans. The resistome features (ARG types, subtypes, indicator ARGs, and emerging mobilizable ARGs: mcr and tet(X)) in these habitats were benchmarked via a standardized workflow. We found that wastewater and wastewater treatment works were characterized to be reservoirs of more diverse genotypes of ARGs than any other habitats including human and livestock fecal samples, while fecal samples were with higher ARG abundance. Bacterial taxonomy composition was significantly correlated with resistome composition across most habitats. Moreover, the source-sink connectivities were disentangled by developing the resistome-based microbial attribution prediction model. Environmental surveys with standardized bioinformatic workflow proposed in this study will help comprehensively understand the transfer of ARGs in the environment, thus prioritizing the critical environments with high risks for intervention to tackle the problem of ARGs.}, }
@article {pmid36996192, year = {2023}, author = {Bruner-Montero, G and Luque, CM and Cesar, CS and Ding, SD and Day, JP and Jiggins, FM}, title = {Hunting Drosophila viruses from wild populations: A novel isolation approach and characterisation of viruses.}, journal = {PLoS pathogens}, volume = {19}, number = {3}, pages = {e1010883}, doi = {10.1371/journal.ppat.1010883}, pmid = {36996192}, issn = {1553-7374}, abstract = {Metagenomic studies have demonstrated that viruses are extremely diverse and abundant in insects, but the difficulty of isolating them means little is known about the biology of these newly discovered viruses. To overcome this challenge in Drosophila, we created a cell line that was more permissive to infection and detected novel viruses by the presence of double-stranded RNA. We demonstrate the utility of these tools by isolating La Jolla virus (LJV) and Newfield virus (NFV) from several wild Drosophila populations. These viruses have different potential host ranges, with distinct abilities to replicate in five Drosophila species. Similarly, in some species they cause high mortality and in others they are comparatively benign. In three species, NFV but not LJV caused large declines in female fecundity. This sterilization effect was associated with differences in tissue tropism, as NFV but not LJV was able to infect Drosophila melanogaster ovaries. We saw a similar effect in the invasive pest of fruit crops Drosophila suzukii, where oral infection with NFV caused reductions in the fecundity, suggesting it has potential as a biocontrol agent. In conclusion, a simple protocol allowed us to isolate new viruses and demonstrate that viruses identified by metagenomics have a large effect on the fitness of the model organism D. melanogaster and related species.}, }
@article {pmid36996123, year = {2023}, author = {Ostenfeld, LJ and Munk, P and Aarestrup, FM and Otani, S}, title = {Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0283676}, doi = {10.1371/journal.pone.0283676}, pmid = {36996123}, issn = {1932-6203}, abstract = {Microbial communities have huge impacts on their ecosystems and local environments spanning from marine and soil communities to the mammalian gut. Bacteriophages (phages) are important drivers of population control and diversity in the community, but our understanding of complex microbial communities is halted by biased detection techniques. Metagenomics have provided a method of novel phage discovery independent of in vitro culturing techniques and have revealed a large proportion of understudied phages. Here, five jumbophage genomes, that were previously assembled in silico from pig faecal metagenomes, are detected and observed directly in their natural environment using a modified phageFISH approach, and combined with methods to decrease bias against large-sized phages (e.g., jumbophages). These phages are uncultured with unknown hosts. The specific phages were detected by PCR and fluorescent in situ hybridisation in their original faecal samples as well as across other faecal samples. Co-localisation of bacterial signals and phage signals allowed detection of the different stages of phage life cycle. All phages displayed examples of early infection, advanced infection, burst, and free phages. To our knowledge, this is the first detection of jumbophages in faeces, which were investigated independently of culture, host identification, and size, and based solely on the genome sequence. This approach opens up opportunities for characterisation of novel in silico phages in vivo from a broad range of gut microbiomes.}, }
@article {pmid36995383, year = {2023}, author = {Nie, S and Jing, Z and Wang, J and Deng, Y and Zhang, Y and Ye, Z and Ge, Y}, title = {The link between increased Desulfovibrio and disease severity in Parkinson's disease.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {36995383}, issn = {1432-0614}, abstract = {Parkinson's disease (PD), a progressive and incurable neurodegenerative disease, has taken a huge economic toll and medical burden on our society. Increasing evidence has shown a strong link between PD and the gut microbiome, but studies on the relationship between the gut microbiome and the severity of PD are limited. In this study, 90 fecal samples were collected from newly diagnosed and untreated patients with PD (n = 47) and matched healthy control subjects (n = 43). The 16S rRNA amplicon and shotgun metagenomic sequencing was performed, aiming to uncover the connection between the gut microbiome and disease severity in PD. The results showed that Desulfovibrio was significantly increased in PD compared to healthy controls and positively correlated with disease severity. The increase in Desulfovibrio was mainly driven by enhanced homogeneous selection and weakened drift. Moreover, through metagenome-assembled genomes (MAGs) analysis, a Desulfovibrio MAG (MAG58) was obtained which was also positively correlated with disease severity. MAG58 possesses a complete assimilatory sulfate reduction pathway and a near-complete dissimilatory sulfate reduction pathway to produce hydrogen sulfide which may influence the development of PD. Based on these results, a potential pathogenic mechanism was presented to illustrate how the increased Desulfovibrio accelerates the development of PD by producing excessive hydrogen sulfide. The present study highlighted the vital role of Desulfovibrio in the development of PD, which may provide a new target for the diagnosis and treatment of PD. KEY POINTS: • The evidence for the link between increased Desulfovibrio and disease severity in PD • A Desulfovibrio MAG was obtained which was correlated with PD • A model was presented to illustrate how increased Desulfovibrio causes PD.}, }
@article {pmid36995244, year = {2023}, author = {Herviou, P and Balvay, A and Bellet, D and Bobet, S and Maudet, C and Staub, J and Alric, M and Leblond-Bourget, N and Delorme, C and Rabot, S and Denis, S and Payot, S}, title = {Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0466722}, doi = {10.1128/spectrum.04667-22}, pmid = {36995244}, issn = {2165-0497}, abstract = {Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.}, }
@article {pmid36995238, year = {2023}, author = {Zhao, X and Sun, C and Jin, M and Chen, J and Xing, L and Yan, J and Wang, H and Liu, Z and Chen, WH}, title = {Enrichment Culture but Not Metagenomic Sequencing Identified a Highly Prevalent Phage Infecting Lactiplantibacillus plantarum in Human Feces.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0434022}, doi = {10.1128/spectrum.04340-22}, pmid = {36995238}, issn = {2165-0497}, abstract = {Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human diseases, but its phages in the human gut remain unexplored. Here, we report its first gut phage, Gut-P1, which we systematically screened using metagenomic sequencing, virus-like particle (VLP) sequencing, and enrichment culture from 35 fecal samples. Gut-P1 is virulent, belongs to the Douglaswolinvirus genus, and is highly prevalent in the gut (~11% prevalence); it has a genome of 79,928 bp consisting of 125 protein coding genes and displaying low sequence similarities to public L. plantarum phages. Physiochemical characterization shows that it has a short latent period and adapts to broad ranges of temperatures and pHs. Furthermore, Gut-P1 strongly inhibits the growth of L. plantarum strains at a multiplicity of infection (MOI) of 1e-6. Together, these results indicate that Gut-P1 can greatly impede the application of L. plantarum in humans. Strikingly, Gut-P1 was identified only in the enrichment culture, not in our metagenomic or VLP sequencing data nor in any public human phage databases, indicating the inefficiency of bulk sequencing in recovering low-abundance but highly prevalent phages and pointing to the unexplored hidden diversity of the human gut virome despite recent large-scale sequencing and bioinformatics efforts. IMPORTANCE As Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human gut-related diseases, its bacteriophages may pose a certain threat to their further application and should be identified and characterized more often from the human intestine. Here, we isolated and identified the first gut L. plantarum phage that is prevalent in a Chinese population. This phage, Gut-P1, is virulent and can strongly inhibit the growth of multiple L. plantarum strains at low MOIs. Our results also show that bulk sequencing is inefficient at recovering low-abundance but highly prevalent phages such as Gut-P1, suggesting that the hidden diversity of human enteroviruses has not yet been explored. Our results call for innovative approaches to isolate and identify intestinal phages from the human gut and to rethink our current understanding of the enterovirus, particularly its underestimated diversity and overestimated individual specificity.}, }
@article {pmid36993673, year = {2023}, author = {Rich, MH and Sharrock, AV and Mulligan, TS and Matthews, F and Brown, AS and Lee-Harwood, HR and Williams, EM and Copp, JN and Little, RF and Francis, JJ and Horvat, CN and Stevenson, LJ and Owen, JG and Saxena, MT and Mumm, JS and Ackerley, DF}, title = {A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.03.24.534183}, pmid = {36993673}, abstract = {Functional screening of environmental DNA (eDNA) libraries is a potentially powerful approach to discover enzymatic "unknown unknowns", but is usually heavily biased toward the tiny subset of genes preferentially transcribed and translated by the screening strain. We have overcome this by preparing an eDNA library via partial digest with restriction enzyme Fatl (cuts CATG), causing a substantial proportion of ATG start codons to be precisely aligned with strong plasmid-encoded promoter and ribosome-binding sequences. Whereas we were unable to select nitroreductases from standard metagenome libraries, our Fatl strategy yielded 21 nitroreductases spanning eight different enzyme families, each conferring resistance to the nitro-antibiotic niclosamide and sensitivity to the nitro-prodrug metronidazole. We showed expression could be improved by co-expressing rare tRNAs and encoded proteins purified directly using an embedded Hisg-tag. In a transgenic zebrafish model of metronidazole-mediated targeted cell ablation, our lead MhqN-family nitroreductase proved ∼5- fold more effective than the canonical nitroreductase NfsB.}, }
@article {pmid36993583, year = {2023}, author = {Holm, JB and France, MT and Gajer, P and Ma, B and Brotman, RM and Shardell, M and Forney, L and Ravel, J}, title = {High-resolution functional description of vaginal microbiomes in health and disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.03.24.533147}, pmid = {36993583}, abstract = {BACKGROUND: A Lactobacillus- dominated vaginal microbiome provides the first line of defense against numerous adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this limitation, we developed metagenomic community state types (mgCSTs) which uses metagenomic sequences to describe and define vaginal microbiomes based on both composition and function.<br><br>RESULTS: MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerella mgSs, as well as a mgSs of L. iners , were associated with a greater likelihood of Amsel bacterial vaginosis diagnosis. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier as an easily applied, standardized method for use by the microbiome research community.<br><br>CONCLUSIONS: MgCSTs are a novel and easily implemented approach to reducing the dimension of complex metagenomic datasets, while maintaining their functional uniqueness. MgCSTs enable investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates protection to the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women&#xe2;&#x20ac;&#x2122;s genital health.}, }
@article {pmid36993556, year = {2023}, author = {Fogarty, EC and Schechter, MS and Lolans, K and Sheahan, ML and Veseli, I and Moore, R and Kiefl, E and Moody, T and Rice, PA and Yu, MK and Mimee, M and Chang, EB and Mclellan, SL and Willis, AD and Comstock, LE and Eren, AM}, title = {A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.03.25.534219}, pmid = {36993556}, abstract = {Plasmids are extrachromosomal genetic elements that often encode fitness enhancing features. However, many bacteria carry 'cryptic' plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes, and is 14 times as numerous as crAssphage, currently established as the most abundant genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales and although it does not appear to impact bacterial host fitness in vivo , can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an inexpensive alternative for detecting human colonic inflammatory states.}, }
@article {pmid36992482, year = {2023}, author = {Wu, Q and Habili, N and Kinoti, WM and Tyerman, SD and Rinaldo, A and Zheng, L and Constable, FE}, title = {A Metagenomic Investigation of the Viruses Associated with Shiraz Disease in Australia.}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/v15030774}, pmid = {36992482}, issn = {1999-4915}, abstract = {Shiraz disease (SD) is an economically important virus-associated disease that can significantly reduce yield in sensitive grapevine varieties and has so far only been reported in South Africa and Australia. In this study, RT-PCR and metagenomic high-throughput sequencing was used to study the virome of symptomatic and asymptomatic grapevines within vineyards affected by SD and located in South Australia. Results showed that grapevine virus A (GVA) phylogroup II variants were strongly associated with SD symptoms in Shiraz grapevines that also had mixed infections of viruses including combinations of grapevine leafroll-associated virus 3 (GLRaV-3) and grapevine leafroll-associated virus 4 strains 5, 6 and 9 (GLRaV-4/5, GLRaV-4/6, GLRaV-4/9). GVA phylogroup III variants, on the other hand, were present in both symptomatic and asymptomatic grapevines, suggesting no or decreased virulence of these strains. Similarly, only GVA phylogroup I variants were found in heritage Shiraz grapevines affected by mild leafroll disease, along with GLRaV-1, suggesting this phylogroup may not be associated with SD.}, }
@article {pmid36992458, year = {2023}, author = {Chen, Z and Zhao, H and Li, Z and Huang, M and Si, N and Zhao, H and Wei, X and Sun, B and Gao, GF and Xu, Z and Liu, WJ}, title = {First Discovery of Phenuiviruses within Diverse RNA Viromes of Asiatic Toad (Bufo gargarizans) by Metagenomics Sequencing.}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/v15030750}, pmid = {36992458}, issn = {1999-4915}, abstract = {Most zoonotic pathogens originate from mammals and avians, but viral diversity and related biosafety risk assessment in lower vertebrates also need to be explored. Amphibians are an important group of lower vertebrates that played a momentous role in animal evolution. To elucidate the diversity of RNA viruses in one important species of amphibians, the Asiatic toad (Bufo gargarizans), we obtained 44 samples including lung, gut, liver, and kidney tissues from Asiatic toads in Sichuan and Jilin provinces, China, for viral metagenomics sequencing. More than 20 novel RNA viruses derived from the order Bunyavirales and 7 families of Astroviridae, Dicistroviridae, Leviviridae, Partitiviridae, Picornaviridae, Rhabdoviridae, and Virgaviridae were discovered, which were distinct from previously described viruses and formed new clusters, as revealed by phylogenetic analyses. Notably, a novel bastrovirus, AtBastV/GCCDC11/2022, of the family Astroviridae was identified from the gut library, the genome of which contains three open reading frames, with the RNA-dependent RNA polymerase (RdRp) coded by ORF1 closely related to that of hepeviruses, and ORF2 encoding an astrovirus-related capsid protein. Notably, phenuiviruses were discovered for the first time in amphibians. AtPhenV1/GCCDC12/2022 and AtPhenV2/GCCDC13/2022 clustered together and formed a clade with the group of phenuiviruses identified from rodents. Picornaviruses and several invertebrate RNA viruses were also detected. These findings improve our understanding of the high RNA viral diversity in the Asiatic toad and provide new insights in the evolution of RNA viruses in amphibians.}, }
@article {pmid36992396, year = {2023}, author = {Wang, H and Li, Z and Li, C and Ma, Y and Sun, Q and Zhang, H and Niu, G and Wei, J and Yao, H and Ma, Z}, title = {Viral Metagenomic Analysis of the Fecal Samples in Domestic Dogs (Canis lupus familiaris).}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/v15030685}, pmid = {36992396}, issn = {1999-4915}, abstract = {Canine diarrhea is a common intestinal illness that is usually caused by viruses, bacteria, and parasites, and canine diarrhea may induce morbidity and mortality of domestic dogs if treated improperly. Recently, viral metagenomics was applied to investigate the signatures of the enteric virome in mammals. In this research, the characteristics of the gut virome in healthy dogs and dogs with diarrhea were analyzed and compared using viral metagenomics. The alpha diversity analysis indicated that the richness and diversity of the gut virome in the dogs with diarrhea were much higher than the healthy dogs, while the beta diversity analysis revealed that the gut virome of the two groups was quite different. At the family level, the predominant viruses in the canine gut virome were certified to be Microviridae, Parvoviridae, Siphoviridae, Inoviridae, Podoviridae, Myoviridae, and others. At the genus level, the predominant viruses in the canine gut virome were certified to be Protoparvovirus, Inovirus, Chlamydiamicrovirus, Lambdavirus, Dependoparvovirus, Lightbulbvirus, Kostyavirus, Punavirus, Lederbergvirus, Fibrovirus, Peduovirus, and others. However, the viral communities between the two groups differed significantly. The unique viral taxa identified in the healthy dogs group were Chlamydiamicrovirus and Lightbulbvirus, while the unique viral taxa identified in the dogs with diarrhea group were Inovirus, Protoparvovirus, Lambdavirus, Dependoparvovirus, Kostyavirus, Punavirus, and other viruses. Phylogenetic analysis based on the near-complete genome sequences showed that the CPV strains collected in this study together with other CPV Chinese isolates clustered into a separate branch, while the identified CAV-2 strain D5-8081 and AAV-5 strain AAV-D5 were both the first near-complete genome sequences in China. Moreover, the predicted bacterial hosts of phages were certified to be Campylobacter, Escherichia, Salmonella, Pseudomonas, Acinetobacter, Moraxella, Mediterraneibacter, and other commensal microbiota. In conclusion, the enteric virome of the healthy dogs group and the dogs with diarrhea group was investigated and compared using viral metagenomics, and the viral communities might influence canine health and disease by interacting with the commensal gut microbiome.}, }
@article {pmid36992315, year = {2023}, author = {Ramos, EDSF and Abreu, WU and Rodrigues, LRR and Marinho, LF and Morais, VDS and Villanova, F and Pandey, RP and Araújo, ELL and Deng, X and Delwart, E and da Costa, AC and Leal, E}, title = {Novel Chaphamaparvovirus in Insectivorous Molossus molossus Bats, from the Brazilian Amazon Region.}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/v15030606}, pmid = {36992315}, issn = {1999-4915}, abstract = {Chaphamaparvovirus (CHPV) is a recently characterized genus of the Parvoviridae family whose members can infect different hosts, including bats, which constitute the second most diverse order of mammals and are described worldwide as important transmitters of zoonotic diseases. In this study, we identified a new CHPV in bat samples from the municipality of Santarém (Pará state, North Brazil). A total of 18 Molossus molossus bats were analyzed using viral metagenomics. In five animals, we identified CHPVs. These CHPV sequences presented the genome with a size ranging from 3797 to 4284 bp. Phylogenetic analysis-based nucleotide and amino acid sequences of the VP1 and NS1 regions showed that all CHPV sequences are monophyletic. They are also closely related to CHPV sequences previously identified in bats in southern and southeast Brazil. According to the International Committee on Taxonomy of Viruses (ICTV) classification criteria for this species (the CHPV NS1 gene region must have 85% identity to be classified in the same species), our sequences are likely a new specie within the genus Chaphamaparvovirus, since they have less than 80% identity with other CHPV described earlier in bats. We also make some phylogenetic considerations about the interaction between CHPV and their host. We suggest a high level of specificity of CPHV and its hosts. Thus, the findings contribute to improving information about the viral diversity of parvoviruses and show the importance of better investigating bats, considering that they harbor a variety of viruses that may favor zoonotic events.}, }
@article {pmid36991496, year = {2023}, author = {Shay, JA and Haniford, LSE and Cooper, A and Carrillo, CD and Blais, BW and Lau, CH}, title = {Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {25}, pmid = {36991496}, issn = {2524-6372}, abstract = {BACKGROUND: With the escalating risk of antimicrobial resistance (AMR), there are limited analytical options available that can comprehensively assess the burden of AMR carried by clinical/environmental samples. Food can be a potential source of AMR bacteria for humans, but its significance in driving the clinical spread of AMR remains unclear, largely due to the lack of holistic-yet-sensitive tools for surveillance and evaluation. Metagenomics is a culture-independent approach well suited for uncovering genetic determinants of defined microbial traits, such as AMR, present within unknown bacterial communities. Despite its popularity, the conventional approach of non-selectively sequencing a sample's metagenome (namely, shotgun-metagenomics) has several technical drawbacks that lead to uncertainty about its effectiveness for AMR assessment; for instance, the low discovery rate of resistance-associated genes due to their naturally small genomic footprint within the vast metagenome. Here, we describe the development of a targeted resistome sequencing method and demonstrate its application in the characterization of the AMR gene profile of bacteria associated with several retail foods.<br><br>RESULT: A targeted-metagenomic sequencing workflow using a customized bait-capture system targeting over 4,000 referenced AMR genes and 263 plasmid replicon sequences was validated against both mock and sample-derived bacterial community preparations. Compared to shotgun-metagenomics, the targeted method consistently provided for improved recovery of resistance gene targets with a much-improved target detection efficiency (>&#x2009;300-fold). Targeted resistome analyses conducted on 36 retail-acquired food samples (fresh sprouts, n&#x2009;=&#x2009;10; ground meat, n&#x2009;=&#x2009;26) and their corresponding bacterial enrichment cultures (n&#x2009;=&#x2009;36) reveals in-depth features regarding the identity and diversity of AMR genes, most of which were otherwise undetected by the whole-metagenome shotgun sequencing method. Furthermore, our findings suggest that foodborne Gammaproteobacteria could be the major reservoir of food-associated AMR genetic determinants, and that the resistome structure of the selected high-risk food commodities are, to a large extent, dictated by microbiome composition.<br><br>CONCLUSIONS: For metagenomic sequencing-based surveillance of AMR, the target-capture method presented herein represents a more sensitive and efficient approach to evaluate the resistome profile of complex food or environmental samples. This study also further implicates retail foods as carriers of diverse resistance-conferring genes indicating a potential impact on the dissemination of AMR.}, }
@article {pmid36991491, year = {2023}, author = {Hénaff, E and Najjar, D and Perez, M and Flores, R and Woebken, C and Mason, CE and Slavin, K}, title = {Holobiont Urbanism: sampling urban beehives reveals cities' metagenomes.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {23}, pmid = {36991491}, issn = {2524-6372}, support = {1R01MH117406/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Over half of the world's population lives in urban areas with, according to the United Nations, nearly 70% expected to live in cities by 2050. Our cities are built by and for humans, but are also complex, adaptive biological systems involving a diversity of other living species. The majority of these species are invisible and constitute the city's microbiome. Our design decisions for the built environment shape these invisible populations, and as inhabitants we interact with them on a constant basis. A growing body of evidence shows us that human health and well-being are dependent on these interactions. Indeed, multicellular organisms owe meaningful aspects of their development and phenotype to interactions with the microorganisms-bacteria or fungi-with which they live in continual exchange and symbiosis. Therefore, it is meaningful to establish microbial maps of the cities we inhabit. While the processing and sequencing of environmental microbiome samples can be high-throughput, gathering samples is still labor and time intensive, and can require mobilizing large numbers of volunteers to get a snapshot of the microbial landscape of a city.<br><br>RESULTS: Here we postulate that honeybees may be effective collaborators in gathering samples of urban microbiota, as they forage daily within a 2-mile radius of their hive. We describe the results of a pilot study conducted with three rooftop beehives in Brooklyn, NY, where we evaluated the potential of various hive materials (honey, debris, hive swabs, bee bodies) to reveal information as to the surrounding metagenomic landscape, and where we conclude that the bee debris are the richest substrate. Based on these results, we profiled 4 additional cities through collected hive debris: Sydney, Melbourne, Venice and Tokyo. We show that each city displays a unique metagenomic profile as seen by honeybees. These profiles yield information relevant to hive health such as known bee symbionts and pathogens. Additionally, we show that this method can be used for human pathogen surveillance, with a proof-of-concept example in which we recover the majority of virulence factor genes for Rickettsia felis, a pathogen known to be responsible for "cat scratch fever".<br><br>CONCLUSIONS: We show that this method yields information relevant to hive health and human health, providing a strategy to monitor environmental microbiomes on a city scale. Here we present the results of this study, and discuss them in terms of architectural implications, as well as the potential of this method for epidemic surveillance.}, }
@article {pmid36991068, year = {2023}, author = {Zhang, C and Liu, X and Shi, LD and Li, J and Xiao, X and Shao, Z and Dong, X}, title = {Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {13}, pmid = {36991068}, issn = {2055-5008}, abstract = {Cold seeps, where cold hydrocarbon-rich fluid escapes from the seafloor, show strong enrichment of toxic metalloid arsenic (As). The toxicity and mobility of As can be greatly altered by microbial processes that play an important role in global As biogeochemical cycling. However, a global overview of genes and microbes involved in As transformation at seeps remains to be fully unveiled. Using 87 sediment metagenomes and 33 metatranscriptomes derived from 13 globally distributed cold seeps, we show that As detoxification genes (arsM, arsP, arsC1/arsC2, acr3) were prevalent at seeps and more phylogenetically diverse than previously expected. Asgardarchaeota and a variety of unidentified bacterial phyla (e.g. 4484-113, AABM5-125-24 and RBG-13-66-14) may also function as the key players in As transformation. The abundances of As cycling genes and the compositions of As-associated microbiome shifted across different sediment depths or types of cold seep. The energy-conserving arsenate reduction or arsenite oxidation could impact biogeochemical cycling of carbon and nitrogen, via supporting carbon fixation, hydrocarbon degradation and nitrogen fixation. Overall, this study provides a comprehensive overview of As cycling genes and microbes at As-enriched cold seeps, laying a solid foundation for further studies of As cycling in deep sea microbiome at the enzymatic and processual levels.}, }
@article {pmid36990699, year = {2023}, author = {Zhou, H}, title = {[Several issues in interpreting the results of metagenomic next generation sequencing of lower respiratory tract infection].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {46}, number = {4}, pages = {319-321}, doi = {10.3760/cma.j.cn112147-20221117-00903}, pmid = {36990699}, issn = {1001-0939}, abstract = {Metagenome next generation sequencing (mNGS) is an important method for pathogen diagnosis of lower respiratory tract infection, but there are many difficulties in interpreting mNGS reports. The Expert Consensus on Clinical Interpretation Path of mNGS of Lower Respiratory Tract Infection, completed by Chinese Thoracic Society, provides a detailed path and guidance for report interpretation. The expert consensus covers clinical medicine, microbiology, molecular diagnosis and other aspects. On this basis, several important clinical issues need to be highlighted. First, the lower respiratory tract specimens used for mNGS must be obtained in a timely and qualified manner. Second, the correct interpretation of the mNGS report needs to be based on a full understanding of the patients and their conditions. Third, the quality of the report should be analyzed according to the main parameters in the mNGS report. Fourth, an understanding of basic microbiology knowledge is beneficial to identify valuable pathogens in the mNGS report. Fifth, other microbiological methods should be actively used during mNGS detection. Sixth, to seek the help of the team when necessary and organize multidisciplinary discussions are vital. Seventh, it is important to constantly adjust the diagnosis and treatment strategies according to the clinical treatment response to treatment and the evolution of the disease. In a word, the interpretation of mNGS results needs to refer to specimen types and sequencing parameters, to combine with the specific conditions of patients in detail, to collect a variety of microbiological test results, to carefully screen and make judgement according to the treatment effect and disease outcome, and finally to make the diagnosis. The interpretation of mNGS report also requires us to have more knowledge of microbiology, sequencing and bioinformatics analysis, and to pay more attention to the strength of the team to discriminate the truth in multidisciplinary collaboration.}, }
@article {pmid36990698, year = {2023}, author = {Lu, BH}, title = {[Basic competence for etiological diagnosis of lower respiratory tract infection after application of metagenomic next-generation sequencing].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {46}, number = {4}, pages = {315-318}, doi = {10.3760/cma.j.cn112147-20221121-00915}, pmid = {36990698}, issn = {1001-0939}, abstract = {In addition to clinical manifestations, medical history, and imaging, the diagnosis of low respiratory tract infection (LRTI) depends mainly on the ability of the clinical microbiology laboratory to detect the pathogens. However, conventional culture may be time-consuming, the sensitivity of microscopy is low, and nucleic acid-based targeted tests (e.g., PCR) could only cover limited range of pathogens. The use of mNGS technology has improved the diagnostic rate of LRTI, but the conventional microbiology detection has been neglected to some extent. This review addressed the appropriate use of these methods with the aim of strengthening the ability of traditional microbiology methods in LRTI diagnosis after mNGS application.}, }
@article {pmid36990697, year = {2023}, author = {Shi, Y and Li, P}, title = {[Diagnostic value and consideration of low sequence pathogens detected by metagenomic next-generation sequencing in lower respiratory tract infection].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {46}, number = {4}, pages = {311-314}, doi = {10.3760/cma.j.cn112147-20221129-00939}, pmid = {36990697}, issn = {1001-0939}, abstract = {Pathogenic diagnosis of lower respiratory tract infection has always been a clinical problem. The widespread application of metagenomic next-generation sequencing(mNGS)provides a rapid and accurate method for pathogenic diagnosis. However, how to interpret the results of mNGS detection, especially whether it has diagnostic value in detecting pathogens with low sequence number, has always puzzled clinicians. This paper discusses the definition of low sequence number (lower reads)detected by mNGS in lower respiratory tract infection, the cause of occurrence, the method to determine the reliability of the results, and how to correctly interpret the low sequence number report in combination with clinical practice. It is hoped that by comprehensively mastering the detection knowledge, the proper clinical analysis thinking can be established to improve the diagnostic ability of pathogens with low sequence number detected by mNGS in lower respiratory tract infection.}, }
@article {pmid36990340, year = {2023}, author = {Qin, G and Zhang, Q and Zhang, Z and Chen, Y and Zhu, J and Yang, Y and Peijnenburg, WJGM and Qian, H}, title = {Understanding the ecological effects of the fungicide difenoconazole on soil and Enchytraeus crypticus gut microbiome.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {121518}, doi = {10.1016/j.envpol.2023.121518}, pmid = {36990340}, issn = {1873-6424}, abstract = {Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress.}, }
@article {pmid36990333, year = {2023}, author = {Su, X and Zhu, XR and Li, J and Wu, L and Li, X and Zhang, Q and Peng, Y}, title = {Determination of partial denitrification kinetic model parameters based on batch tests and metagenomic sequencing.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {128977}, doi = {10.1016/j.biortech.2023.128977}, pmid = {36990333}, issn = {1873-2976}, abstract = {In this study, a model was developed to investigate the partial denitrification(PD) process. The heterotrophic biomass (XH) proportion in the sludge was determined to be 66.4% based on metagenomic sequencing. The kinetic parameters were first calibrated, then validated using the batch tests results . The results showed rapid decreases in the chemical oxygen demand (COD) and nitrate concentrations and gradual increases in the nitrite concentrations in the first four hours, then remained constant from 4 to 8 h. Anoxic reduction factor (ηNO3 and ηNO2) and half saturation constant (KS1 and KS2) were calibrated at 0.097, 0.13, 89.28 mg COD/L, and 102.29 mg COD/L, respectively. Whereas the simulation results demonstrated that the increase in carbon-to-nitrogen (C/N) ratios and the reduction in XH contributed to the increase in the nitrite transformation rate. This model provides potential strategies for optimizing the PD/A process.}, }
@article {pmid36990280, year = {2023}, author = {Pyden, A and Rugwizangoga, B and Solomon, IH and Laga, AC}, title = {`Teaching Infectious Disease Pathology and Taking it To Africa.}, journal = {Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc}, volume = {}, number = {}, pages = {100168}, doi = {10.1016/j.modpat.2023.100168}, pmid = {36990280}, issn = {1530-0285}, abstract = {With the advent of increasing emerging infectious diseases, rising antibiotic resistance, and the growing number of immunocompromised patients, there is increasing demand for infectious disease (ID) pathology expertise and microbiology testing. At present, infectious disease pathology training and emerging molecular microbiology techniques (e.g. metagenomic next-generation sequencing and whole genome sequencing) are not included in most American Council of Graduate Medical Education (ACGME) medical microbiology fellowship curricula, and, not surprisingly, many institutions lack anatomic pathologists with expertise in ID pathology and advanced molecular diagnostics. In this article, we describe the curriculum and structure of the Franz von Lichtenberg Fellowship in Infectious Disease and Molecular Microbiology at Brigham and Women's Hospital in Boston, MA. We emphasize the value of a training model that strives to integrate anatomic pathology, clinical pathology, and molecular pathology by providing examples in a case-based format and presenting selected metrics of the potential impact of such integrative infectious disease pathology service, and briefly describing opportunities and challenges of our global health efforts in Rwanda.}, }
@article {pmid36990236, year = {2023}, author = {Xiang, R and Tian, Z and Zhang, C and Zheng, B and Jia, H}, title = {Characterization of dissolved organic matter content, composition, and source during spring algal bloom in tributaries of the Three Gorges Reservoir.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163139}, doi = {10.1016/j.scitotenv.2023.163139}, pmid = {36990236}, issn = {1879-1026}, abstract = {Dissolved organic matter (DOM) is a key component of aquatic ecosystem function and biogeochemical processes. The characteristics of DOM in tributaries of the Three Gorges Reservoir (TGR) during the severe spring algal bloom period and their relationship with algal growth are unclear. In this study, the content, composition, and source of DOM in the Pengxi River (PXR) and Ruxi River (RXR) exhibiting typical TGR bloom problems were analyzed using various physicochemical indexes, carbon isotopes, fatty acids, and metagenomics. The results showed that chlorophyll a content increased with rising DOM concentration in the PXR and RXR. The dissolved organic carbon (DOC) and chromophoric dissolved organic matter (CDOM) contents in the two rivers were 4.656-16.560 mg/L and 14.373-50.848 μg/L, respectively, and increased during the bloom period. Four fluorescent components were identified, namely, two humic-like substances, and two protein-like substances. Proteobacteria, bacteroidetes, and actinobacteria were the greatest contributors to DOM content. The carbon fixation pathway of microorganisms increased the DOC concentration in both rivers during the bloom period. Physicochemical parameters (WT, pH, DO, and PAR) affected the DOM concentration by influencing microbial activity and DOM degradation. DOM in both rivers was derived from allochthonous and autogenous sources. Meanwhile, the DOC content was more strongly correlated with allochthonous sources. These findings might provide essential information for improving water environment management and algal bloom control in the TGR.}, }
@article {pmid36990166, year = {2023}, author = {Yang, H and Wu, C and Chen, L and Chang, X and Luo, G and Wu, K and Tian, W}, title = {A. macrocephala polysaccharide induces alterations to gut microbiome and serum metabolome in constipated mice.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {106084}, doi = {10.1016/j.micpath.2023.106084}, pmid = {36990166}, issn = {1096-1208}, abstract = {Atractylodes macrocephala polysaccharide (AC1) is extracted from the root of the Chinese herb Atractylodes Macrocephala and is used in the treatment of constipation due to its effects on strengthening cellular immunity and regulating intestinal function. In this study, Metagenomics and Metabolomic are used to analyze the effects of AC1 on the gut microbiota and host metabolites in mice models of constipation. The results show that the abundance of Lachnospiraceae_bacterium_A4, Bact-oides_vulgatus and Prevotella_sp_CAG:891 increased significantly, indicating that AC1-targeted strain modulation effectively alleviated the dysbiosis of the gut microbiota. Besides, the microbial alterations also influenced the metabolic pathways of the mice, including tryptophan metabolism, unsaturated fatty acid synthesis and bile acid metabolism. The physiological parameters of the mice treated with AC1 are improved, such as tryptophan in the colon, 5-hydroxytryptamine (5-HT) and short-chain fatty acids (SCFAs). In conclusion, AC1 as a probiotic can regulate intestinal flora to normal levels and achieve the effect of treating constipation.}, }
@article {pmid36989806, year = {2023}, author = {Yan, Y and Zhang, J and Tian, L and Yan, X and Du, L and Leininger, A and Zhang, M and Li, N and Ren, ZJ and Wang, X}, title = {DIET-like mutualism of Geobacter and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate.}, journal = {Water research}, volume = {235}, number = {}, pages = {119911}, doi = {10.1016/j.watres.2023.119911}, pmid = {36989806}, issn = {1879-2448}, abstract = {Direct interspecies electron transfer (DIET) has been demonstrated to be an efficient type of mutualism in methanogenesis. However, few studies have reported its presence in mixed microbial communities and its trigger mechanism in the natural environment and engineered systems. Here, we reported DIET-like mutualism of Geobacter and methanogens in the planktonic microbiome for the first time in anaerobic electrochemical digestion (AED) fed with propionate, potentially triggered by excessive cathodic hydrogen (56 times higher than the lowest) under the electrochemical condition. In contrast with model prediction without DIET, the highest current density and hydrogen and methane production were concurrently observed at -0.2 V where an abundance of Geobacter (49%) and extracellular electron transfer genes were identified in the planktonic microbiome via metagenomic analysis. Metagenomic assembly genomes annotated to Geobacter anodireducens were identified alongside two methanogens, Methanothrix harundinacea and Methanosarcina mazei, which were previously identified to participate in DIET. This discovery revealed that DIET-like mutualism could be triggered without external conductive materials, highlighting its potentially ubiquitous presence. Such mutualism simultaneously boosted methane and hydrogen production, thereby demonstrating the potential of AED in engineering applications.}, }
@article {pmid36989799, year = {2023}, author = {Calderón-Franco, D and Corbera-Rubio, F and Cuesta-Sanz, M and Pieterse, B and de Ridder, D and van Loosdrecht, MCM and van Halem, D and Laureni, M and Weissbrodt, DG}, title = {Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems.}, journal = {Water research}, volume = {235}, number = {}, pages = {119905}, doi = {10.1016/j.watres.2023.119905}, pmid = {36989799}, issn = {1879-2448}, abstract = {Drinking water treatment plants (DWTPs) are designed to remove physical, chemical, and biological contaminants. However, until recently, the role of DWTPs in minimizing the cycling of antibiotic resistance determinants has got limited attention. In particular, the risk of selecting antibiotic-resistant bacteria (ARB) is largely overlooked in chlorine-free DWTPs where biological processes are applied. Here, we combined high-throughput quantitative PCR and metagenomics to analyze the abundance and dynamics of microbial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) across the treatment trains of two chlorine-free DWTPs involving dune-based and reservoir-based systems. The microbial diversity of the water increased after all biological unit operations, namely rapid and slow sand filtration (SSF), and granular activated carbon filtration. Both DWTPs reduced the concentration of ARGs and MGEs in the water by circa 2.5 log gene copies mL[-1], despite their relative increase in the disinfection sub-units (SSF in dune-based and UV treatment in reservoir-based DWTPs). The total microbial concentration was also reduced (2.5 log units), and none of the DWTPs enriched for bacteria containing genes linked to antibiotic resistance. Our findings highlight the effectiveness of chlorine-free DWTPs in supplying safe drinking water while reducing the concentration of antibiotic resistance determinants. To the best of our knowledge, this is the first study that monitors the presence and dynamics of antibiotic resistance determinants in chlorine-free DWTPs.}, }
@article {pmid36989208, year = {2023}, author = {Rajamanikam, A and Isa, MNM and Samudi, C and Devaraj, S and Govind, SK}, title = {Gut bacteria influence Blastocystis sp. phenotypes and may trigger pathogenicity.}, journal = {PLoS neglected tropical diseases}, volume = {17}, number = {3}, pages = {e0011170}, doi = {10.1371/journal.pntd.0011170}, pmid = {36989208}, issn = {1935-2735}, abstract = {Whilst the influence of intestinal microbiota has been shown in many diseases such as irritable bowel syndrome, colorectal cancer, and aging, investigations are still scarce on its role in altering the nature of other infective organisms. Here we studied the association and interaction of Blastocystis sp. and human intestinal microbiota. In this study, we investigated the gut microbiome of Blastocystis sp.-free and Blastocystis sp. ST3-infected individuals who are symptomatic and asymptomatic. We tested if the expression of phenotype and pathogenic characteristics of Blastocystis sp. ST3 was influenced by the alteration of its accompanying microbiota. Blastocystis sp. ST3 infection alters bacterial composition. Its presence in asymptomatic individuals showed a significant effect on microbial richness compared to symptomatic ones. Inferred metagenomic findings suggest that colonization of Blastocystis sp. ST3 could contribute to the alteration of microbial functions. For the first time, we demonstrate the influence of bacteria on Blastocystis sp. pathogenicity. When Blastocystis sp. isolated from a symptomatic individual was co-cultured with bacterial suspension of Blastocystis sp. from an asymptomatic individual, the parasite demonstrated increased growth and reduced potential pathogenic expressions. This study also reveals that Blastocystis sp. infection could influence microbial functions without much effect on the microbiota diversity itself. Our results also demonstrate evidence on the influential role of gut microbiota in altering the characteristics of the parasite, which becomes the basis for the contradictory findings on the parasite's pathogenic role seen across different studies. Our study provides evidence that asymptomatic Blastocystis sp. in a human gut can be triggered to show pathogenic characteristics when influenced by the intestinal microbiota.}, }
@article {pmid36988865, year = {2023}, author = {Xu, J and Zhou, P and Liu, J and Zhao, L and Fu, H and Han, Q and Wang, L and Wu, W and Ou, Q and Ma, Y and He, J}, title = {Utilizing Metagenomic Next-Generation Sequencing (mNGS) for Rapid Pathogen Identification and to Inform Clinical Decision-Making: Results from a Large Real-World Cohort.}, journal = {Infectious diseases and therapy}, volume = {}, number = {}, pages = {}, pmid = {36988865}, issn = {2193-8229}, abstract = {INTRODUCTION: Clinical metagenomic next-generation sequencing (mNGS) has proven to be a powerful diagnostic tool in pathogen detection. However, its clinical utility has not been thoroughly evaluated.<br><br>METHODS: In this single-center prospective study at the First Affiliated Hospital of Soochow University, a total of 228 samples from 215 patients suspected of having acute or chronic infections between June 2018 and December 2018 were studied. Samples that met the mNGS quality control (QC) criteria (N&#x2009;=&#x2009;201) were simultaneously analyzed using conventional tests (CTs), including multiple clinical microbiological tests and real-time PCR (if applicable).<br><br>RESULTS: Pathogen detection results of mNGS in the 201 QC-passed samples were compared to CTs and exhibited a sensitivity of 98.8%, specificity of 38.5%, and accuracy of 87.1%. Specifically, 109 out of 160 (68.1%) CT+/mNGS+&#x2009;samples exhibited concordant results at the species/genus level, 25 samples (15.6%) showed overlapping results, while the remaining 26 samples (16.3%) had discordant results between the CT and mNGS assays. In addition, mNGS could identify pathogens at the species level, whereas only the genera of some pathogens could be identified by CT. In this cohort, mNGS results were used to guide treatment plans in 24 out of 41 cases that had available follow-up information, and the symptoms were improved in over 70% (17/24) of them.<br><br>CONCLUSION: Our data demonstrated the analytic performance of our mNGS pipeline for pathogen detection using a large clinical cohort and strongly supports the notion that in clinical practice, mNGS represents a valuable supplementary tool to CTs to rapidly determine etiological factors of various types of infection and to guide treatment decision-making.}, }
@article {pmid36987093, year = {2023}, author = {Ventimiglia, M and Castellacci, M and Usai, G and Vangelisti, A and Simoni, S and Natali, L and Cavallini, A and Mascagni, F and Giordani, T}, title = {Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/plants12061405}, pmid = {36987093}, issn = {2223-7747}, abstract = {Genome divergence by repeat proliferation and/or loss is a process that plays a crucial role in species evolution. Nevertheless, knowledge of the variability related to repeat proliferation among species of the same family is still limited. Considering the importance of the Asteraceae family, here we present a first contribution towards the metarepeatome of five Asteraceae species. A comprehensive picture of the repetitive components of all genomes was obtained by genome skimming with Illumina sequence reads and by analyzing a pool of full-length long terminal repeat retrotransposons (LTR-REs). Genome skimming allowed us to estimate the abundance and variability of repetitive components. The structure of the metagenome of the selected species was composed of 67% repetitive sequences, of which LTR-REs represented the bulk of annotated clusters. The species essentially shared ribosomal DNA sequences, whereas the other classes of repetitive DNA were highly variable among species. The pool of full-length LTR-REs was retrieved from all the species and their age of insertion was established, showing several lineage-specific proliferation peaks over the last 15-million years. Overall, a large variability of repeat abundance at superfamily, lineage, and sublineage levels was observed, indicating that repeats within individual genomes followed different evolutionary and temporal dynamics, and that different events of amplification or loss of these sequences may have occurred after species differentiation.}, }
@article {pmid36985385, year = {2023}, author = {García-Maldonado, JQ and Latisnere-Barragán, H and Escobar-Zepeda, A and Cadena, S and Ramírez-Arenas, PJ and Vázquez-Juárez, R and Rojas-Contreras, M and López-Cortés, A}, title = {Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030812}, pmid = {36985385}, issn = {2076-2607}, abstract = {Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments.}, }
@article {pmid36985376, year = {2023}, author = {Baev, V and Apostolova, E and Gotcheva, V and Koprinarova, M and Papageorgiou, M and Rocha, JM and Yahubyan, G and Angelov, A}, title = {16S-rRNA-Based Metagenomic Profiling of the Bacterial Communities in Traditional Bulgarian Sourdoughs.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030803}, pmid = {36985376}, issn = {2076-2607}, abstract = {Sourdoughs (SDs) are spontaneously formed microbial ecosystems composed of various species of lactic acid bacteria (LAB) and acid-tolerant yeasts in food matrices of cereal flours mixed with water. To date, more than 90 LAB species have been isolated, significantly impacting the organoleptic characteristics, shelf life, and health properties of bakery products. To learn more about the unique bacterial communities involved in creating regional Bulgarian sourdoughs, we examined the metacommunities of five sourdoughs produced by spontaneous fermentation and maintained by backslopping in bakeries from three geographic locations. The 16S rRNA gene amplicon sequencing showed that the former genus Lactobacillus was predominant in the studied sourdoughs (51.0-78.9%). Weissella (0.9-42.8%), Herbaspirillum (1.6-3.8%), Serratia (0.1-11.7%), Pediococcus (0.2-7.5%), Bacteroides (0.1-1.3%), and Sphingomonas (0.1-0.5%) were also found in all 5 samples. Genera Leuconostoc, Enterococcus, Bacillus, and Asaia were sample-specific. It is interesting to note that the genus Weissella was more abundant in wholegrain samples. The greatest diversity at the species level was found in the former genus Lactobacillus, presented in the sourdough samples with 13 species. The UPGMA cluster analysis clearly demonstrated similarity in species' relative abundance between samples from the same location. In addition, we can conclude that the presence of two main clusters-one including samples from mountainous places (the cities of Smolyan and Bansko) and the other including samples from the city of Ruse (the banks of the Danube River)-may indicate the impact of climate and geographic location (e.g., terrain, elevation, land use, and nearby water bodies and their streams) on the abundance of microbiome taxa. As the bacterial population is crucial for bread standardization, we expect the local bakery sector to be interested in the relationship between process variables and their effect on bacterial dynamics described in this research study.}, }
@article {pmid36985338, year = {2023}, author = {Xiao, Y and Zhang, P and Zhang, H and Wang, H and Min, G and Wang, H and Wang, Y and Xu, J}, title = {Effects of Resource Availability and Antibiotic Residues on Intestinal Antibiotic Resistance in Bellamya aeruginosa.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030765}, pmid = {36985338}, issn = {2076-2607}, abstract = {Widespread and inappropriate use of antibiotics has been shown to increase the spread of antibiotics and antimicrobial resistance genes (ARGs) in aquatic environments and organisms. Antibiotic use for the treatment of human and animal diseases is increasing continuously globally. However, the effects of legal antibiotic concentrations on benthic consumers in freshwater environments remain unclear. In the present study, we tested the growth response of Bellamya aeruginosa to florfenicol (FF) for 84 days under high and low concentrations of sediment organic matter (carbon [C] and nitrogen [N]). We characterized FF and sediment organic matter impact on the bacterial community, ARGs, and metabolic pathways in the intestine using metagenomic sequencing and analysis. The high concentrations of organic matter in the sediment impacted the growth, intestinal bacterial community, intestinal ARGs, and microbiome metabolic pathways of B. aeruginosa. B. aeruginosa growth increased significantly following exposure to high organic matter content sediment. Proteobacteria, at the phylum level, and Aeromonas at the genus level, were enriched in the intestines. In particular, fragments of four opportunistic pathogens enriched in the intestine of high organic matter content sediment groups, Aeromonas hydrophila, Aeromonas caviae, Aeromonas veronii, and Aeromonas salmonicida, carried 14 ARGs. The metabolic pathways of the B. aeruginosa intestine microbiome were activated and showed a significant positive correlation with sediment organic matter concentrations. In addition, genetic information processing and metabolic functions may be inhibited by the combined exposure to sediment C, N, and FF. The findings of the present study suggest that antibiotic resistance dissemination from benthic animals to the upper trophic levels in freshwater lakes should be studied further.}, }
@article {pmid36985314, year = {2023}, author = {Lozano, FM and Lledó, B and Morales, R and Cascales, A and Hortal, M and Bernabeu, A and Bernabeu, R}, title = {Characterization of the Endometrial Microbiome in Patients with Recurrent Implantation Failure.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030741}, pmid = {36985314}, issn = {2076-2607}, abstract = {An abnormal endometrial microbiota has been associated with implantation failure; therefore, it may be important to evaluate it in order to improve reproductive outcomes in infertile patients. The main objective of our study was to compare the endometrial microbiome of patients with recurrent implantation failure (RIF) and control patients undergoing assisted reproduction treatment (ART). A prospective cohort study including forty-five patients with their own or donated gametes. The endometrial microbiome was analysed by massive sequencing of the bacterial 16S rRNA gene. Different bacterial communities were detected in RIF and control patients. Lactobacillus stands out as the most frequent genus, with 92.27% in RIF patients and 97.96% in control patients, and significant differences were reported between the two groups (p = 0.002). No significant differences were found regarding alpha diversity index. In beta diversity analysis, a significant trend was observed in the separation of the bacterial community between established groups (p < 0.07). Relative abundance analysis identified genera Prevotella (p < 0.001), Streptococcus (p < 0.001), Bifidobacterium (p = 0.002), Lactobacillus (p = 0.002) and Dialister (p = 0.003). Our results demonstrated the existence of an endometrial microbiota characteristic of RIF patients and showed that there might be a relationship between population of the endometrial microbiome and embryo implantation failure, providing us the possibility to improve clinical results in this patients.}, }
@article {pmid36985295, year = {2023}, author = {Goma-Tchimbakala, EJCD and Pietrini, I and Goma-Tchimbakala, J and Corgnati, SP}, title = {Use of Shotgun Metagenomics to Assess the Microbial Diversity and Hydrocarbons Degrading Functions of Auto-Mechanic Workshops Soils Polluted with Gasoline and Diesel Fuel.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030722}, pmid = {36985295}, issn = {2076-2607}, abstract = {Bioaugmentation is a valuable technique for oil recovery. This study investigates the composition and functions of microbial communities in gasoline- and diesel-contaminated soils of garages Matoko (SGM) and Guy et Paul (SGP) originating from auto mechanic workshops as well as the concentration of soil enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase. The work aimed to evaluate the presence of petroleum-hydrocarbon-degrading bacteria for the development of foreseen bioremediation of oil-contaminated soils. Microbial diversity, as given by shotgun metagenomics, indicated the presence of 16 classes, among which Actinobacteria and Gammaproteobacteria dominated, as well as more than 50 families, including the dominant Gordoniaceae (26.63%) in SGM and Pseudomonadaceae (57.89%) in SGP. The dominant bacterial genera in the two soils were, respectively, Gordonia (26.7%) and Pseudomonas (57.9%). The exploration of the bacterial metabolic abilities using HUMANn2 allowed to detect genes and pathways involved in alkanes and aromatic hydrocarbons in the two contaminated soils. Furthermore, enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase were found in high concentrations ranging between 90.27 ± 5.3 and 804.17 ± 20.5 µg pN/g soil/h, which indicated active microbial metabolism. The high diversity of microorganisms with a hydrocarbon degradation genetic package revealed that the bacteria inhabiting the two soils are likely good candidates for the bioaugmentation of oil-contaminated soils.}, }
@article {pmid36985280, year = {2023}, author = {Jamwal, VL and Rather, IA and Ahmed, S and Kumar, A and Gandhi, SG}, title = {Changing Rhizosphere Microbial Community and Metabolites with Developmental Stages of Coleus barbatus.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030705}, pmid = {36985280}, issn = {2076-2607}, abstract = {Coleus barbatus is a medicinal herb belonging to Lamiaceae. It is the only living organism known to produce forskolin, which is a labdane diterpene and is reported to activate adenylate cyclase. Microbes associated with plants play an important role in maintaining plant health. Recently, the targeted application of beneficial plant-associated microbes and their combinations in abiotic and biotic stress tolerance has gained momentum. In this work, we carried out the rhizosphere metagenome sequencing of C. barbatus at different developmental stages to understand how rhizosphere microflora are affected by and affect the metabolite content in plants. We found that the Kaistobacter genus was abundantly present in the rhizosphere of C. barbatus and its accumulation pattern appears to correlate with the quantities of forskolin in the roots at different developmental stages. Members of the Phoma genus, known for several pathogenic species, were in lower numbers in the C. barbatus rhizosphere in comparison with C. blumei. To our knowledge, this is the first metagenomic study of the rhizospheric microbiome of C. barbatus, which may help to explore and exploit the culturable and non-culturable microbial diversity present in the rhizosphere.}, }
@article {pmid36985245, year = {2023}, author = {Cruz-Silva, A and Laureano, G and Pereira, M and Dias, R and Silva, JMD and Oliveira, N and Gouveia, C and Cruz, C and Gama-Carvalho, M and Alagna, F and Duarte, B and Figueiredo, A}, title = {A New Perspective for Vineyard Terroir Identity: Looking for Microbial Indicator Species by Long Read Nanopore Sequencing.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030672}, pmid = {36985245}, issn = {2076-2607}, abstract = {Grapevine is one of the most important fruit crops worldwide, being Portugal one of the top wine producers. It is well established that wine sensory characteristics from a particular region are defined by the physiological responses of the grapevine to its environment and thus, the concept of terroir in viticulture was established. Among all the factors that contribute to terroir definition, soil microorganisms play a major role from nutrient recycling to a drastic influence on plant fitness (growth and protection) and of course wine production. Soil microbiome from four different terroirs in Quinta dos Murças vineyard was analysed through long-read Oxford Nanopore sequencing. We have developed an analytical pipeline that allows the identification of function, ecologies, and indicator species based on long read sequencing data. The Douro vineyard was used as a case study, and we were able to establish microbiome signatures of each terroir.}, }
@article {pmid36985231, year = {2023}, author = {Bandarupalli, VVK and St-Pierre, B}, title = {Metagenomics-Based Analysis of Candidate Lactate Utilizers from the Rumen of Beef Cattle.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030658}, pmid = {36985231}, issn = {2076-2607}, abstract = {In ruminant livestock production, ruminal acidosis is an unintended consequence of the elevated dietary intake of starch-rich feedstuffs. The transition from a state of subacute acidosis (SARA) to acute acidosis is due in large part to the accumulation of lactate in the rumen, which is a consequence of the inability of lactate utilizers to compensate for the increased production of lactate. In this report, we present the 16S rRNA gene-based identification of two bacterial operational taxonomic units (OTUs), Bt-01708_Bf (89.0% identical to Butyrivibrio fibrisolvens) and Bt-01899_Ap (95.3% identical to Anaerococcus prevotii), that were enriched from rumen fluid cultures in which only lactate was provided as an exogenous substrate. Analyses of in-silico-predicted proteomes from metagenomics-assembled contigs assigned to these candidate ruminal bacterial species (Bt-01708_Bf: 1270 annotated coding sequences, 1365 hypothetical coding sequences; Bt-01899_Ap: 871 annotated coding sequences, 1343 hypothetical coding sequences) revealed genes encoding lactate dehydrogenase, a putative lactate transporter, as well as pathways for the production of short chain fatty acids (formate, acetate and butyrate) and for the synthesis of glycogen. In contrast to these shared functions, each OTU also exhibited distinct features, such as the potential for the utilization of a diversified set of small molecules as substrates (Bt-01708_Bf: malate, quinate, taurine and polyamines) or for the utilization of starch (Bt-01899_Ap: alpha-amylase enzymes). Together, these results will contribute to the continued characterization of ruminal bacterial species that can metabolize lactate into distinct subgroups based on other metabolic capabilities.}, }
@article {pmid36985222, year = {2023}, author = {Yongsawas, R and In-On, A and Inta, A and Kampuansai, J and Pandith, H and Suwannarach, N and Lumyong, S and Chitov, T and Disayathanoowat, T}, title = {Bacterial Communities in Lanna Fermented Soybeans from Three Different Ethnolinguistic Groups in Northern Thailand.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030649}, pmid = {36985222}, issn = {2076-2607}, abstract = {Northern Thailand, the main part of the Lanna region, is home to a diverse range of ethnic groups, each with their own food and cultural heritage. The bacterial compositions in fermented soybean (FSB) products indigenous to three Lanna ethnolinguistic groups, including Karen, Lawa, and Shan, were investigated in this study. Bacterial DNA was extracted from the FSB samples and subjected to 16S rRNA gene sequencing using the Illumina sequencing platform. Metagenomic data showed that the predominant bacteria in all FSBs were members of the genus Bacillus (49.5-86.8%), and the Lawa FSB had the greatest bacterial diversity. The presence of genera Ignatzschineria, Yaniella, Atopostipes in the Karen and Lawa FSBs and Proteus in the Shan FSB might be indicators of food hygiene problems during processing. The network analysis predicted antagonistic effects of Bacillus against some indicator and pathogenic bacteria. The functional prediction revealed some potential functional properties of these FSBs. The presence of Bacillus in all FSBs and Vagococcus in the Shan FSB suggests that these FSBs could potentially be good sources of beneficial bacteria, and they should be conserved and promoted for health and food security reasons. However, food processing hygiene measures should be introduced and monitored to warrant their properties as health foods.}, }
@article {pmid36985129, year = {2023}, author = {Slobodkin, AI and Ratnikova, NM and Slobodkina, GB and Klyukina, AA and Chernyh, NA and Merkel, AY}, title = {Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030555}, pmid = {36985129}, issn = {2076-2607}, abstract = {The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood-Ljungdahl pathway for autotrophic CO2 fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide.}, }
@article {pmid36985120, year = {2023}, author = {Guo, Y and Yuan, W and Lyu, N and Pan, Y and Cao, X and Wang, Y and Han, Y and Zhu, B}, title = {Association Studies on Gut and Lung Microbiomes in Patients with Lung Adenocarcinoma.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/microorganisms11030546}, pmid = {36985120}, issn = {2076-2607}, abstract = {Lung adenocarcinoma (LADC) is a prevalent type of lung cancer that is associated with lung and gut microbiota. However, the interactions between these microbiota and cancer development remain unclear. In this study, a microbiome study was performed on paired fecal and bronchoalveolar lavage fluid (BALF) samples from 42 patients with LADC and 64 healthy controls using 16S rRNA gene amplicon and shotgun metagenome sequencing, aiming to correlate the lung and gut microbiota with LADC. Patients with LADC had reduced α-diversity in the gut microbiome and altered β-diversity compared with healthy controls, and the abundances of Flavonifractor, Eggerthella, and Clostridium were higher in the gut microbiome of LADC patients. The increased abundance of microbial species, such as Flavonifractor plautii, was associated with advanced-stage LADC and a higher metastasis rate. Phylogenetically, Haemophilus parainfluenzae was the most frequently shared taxon in the lung and gut microbiota of LADC patients. Gut microbiome functional pathways involving leucine, propanoate, and fatty acids were associated with LADC progression. In conclusion, the low diversity of the gut microbiota and the presence of H. parainfluenzae in gut and lung microbiota were linked to LADC development, while an increased abundance of F. plautii and the enriched metabolic pathways could be associated with the progression of LADC.}, }
@article {pmid36984841, year = {2023}, author = {Cohen, CC and Huneault, H and Accardi, CJ and Jones, DP and Liu, K and Maner-Smith, KM and Song, M and Welsh, JA and Ugalde-Nicalo, PA and Schwimmer, JB and Vos, MB}, title = {Metabolome × Microbiome Changes Associated with a Diet-Induced Reduction in Hepatic Fat among Adolescent Boys.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030401}, pmid = {36984841}, issn = {2218-1989}, support = {UL1TR001442/TR/NCATS NIH HHS/United States ; UL1TR001442/TR/NCATS NIH HHS/United States ; P30ES019776/ES/NIEHS NIH HHS/United States ; P20GM103436/GM/NIGMS NIH HHS/United States ; P20GM113226/GM/NIGMS NIH HHS/United States ; P20GM106396/GM/NIGMS NIH HHS/United States ; T32DK07658/DK/NIDDK NIH HHS/United States ; F32DK131757/DK/NIDDK NIH HHS/United States ; R01DK125701/DK/NIDDK NIH HHS/United States ; R01NR019083/NR/NINR NIH HHS/United States ; }, abstract = {Dietary sugar reduction is one therapeutic strategy for improving nonalcoholic fatty liver disease (NAFLD), and the underlying mechanisms for this effect warrant further investigation. Here, we employed metabolomics and metagenomics to examine systemic biological adaptations associated with dietary sugar restriction and (subsequent) hepatic fat reductions in youth with NAFLD. Data/samples were from a randomized controlled trial in adolescent boys (11-16 years, mean ± SD: 13.0 ± 1.9 years) with biopsy-proven NAFLD who were either provided a low free-sugar diet (LFSD) (n = 20) or consumed their usual diet (n = 20) for 8 weeks. Plasma metabolomics was performed on samples from all 40 participants by coupling hydrophilic interaction liquid chromatography (HILIC) and C18 chromatography with mass spectrometry. In a sub-sample (n = 8 LFSD group and n = 10 usual diet group), 16S ribosomal RNA (rRNA) sequencing was performed on stool to examine changes in microbial composition/diversity. The diet treatment was associated with differential expression of 419 HILIC and 205 C18 metabolite features (p < 0.05), which were enriched in amino acid pathways, including methionine/cysteine and serine/glycine/alanine metabolism (p < 0.05), and lipid pathways, including omega-3 and linoleate metabolism (p < 0.05). Quantified metabolites that were differentially changed in the LFSD group, compared to usual diet group, and representative of these enriched metabolic pathways included increased serine (p = 0.001), glycine (p = 0.004), 2-aminobutyric acid (p = 0.012), and 3-hydroxybutyric acid (p = 0.005), and decreased linolenic acid (p = 0.006). Microbiome changes included an increase in richness at the phylum level and changes in a few genera within Firmicutes. In conclusion, the LFSD treatment, compared to usual diet, was associated with metabolome and microbiome changes that may reflect biological mechanisms linking dietary sugar restriction to a therapeutic decrease in hepatic fat. Studies are needed to validate our findings and test the utility of these "omics" changes as response biomarkers.}, }
@article {pmid36984783, year = {2023}, author = {Fu, X and Zhang, M and Yuan, Y and Chen, Y and Ou, Z and Hashim, Z and Hashim, JH and Zhang, X and Zhao, Z and Norbäck, D and Sun, Y}, title = {Microbial Virulence Factors, Antimicrobial Resistance Genes, Metabolites, and Synthetic Chemicals in Cabins of Commercial Aircraft.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/metabo13030343}, pmid = {36984783}, issn = {2218-1989}, abstract = {Passengers are at a higher risk of respiratory infections and chronic diseases due to microbial exposure in airline cabins. However, the presence of virulence factors (VFs), antimicrobial resistance genes (ARGs), metabolites, and chemicals are yet to be studied. To address this gap, we collected dust samples from the cabins of two airlines, one with textile seats (TSC) and one with leather seats (LSC), and analyzed the exposure using shotgun metagenomics and LC/MS. Results showed that the abundances of 17 VFs and 11 risk chemicals were significantly higher in TSC than LSC (p < 0.01). The predominant VFs in TSC were related to adherence, biofilm formation, and immune modulation, mainly derived from facultative pathogens such as Haemophilus parainfluenzae and Streptococcus pneumoniae. The predominant risk chemicals in TSC included pesticides/herbicides (carbofuran, bromacil, and propazine) and detergents (triethanolamine, diethanolamine, and diethyl phthalate). The abundances of these VFs and detergents followed the trend of TSC > LSC > school classrooms (p < 0.01), potentially explaining the higher incidence of infectious and chronic inflammatory diseases in aircraft. The level of ARGs in aircraft was similar to that in school environments. This is the first multi-omic survey in commercial aircraft, highlighting that surface material choice is a potential intervention strategy for improving passenger health.}, }
@article {pmid36983633, year = {2023}, author = {Kartti, S and Bendani, H and Boumajdi, N and Bouricha, EM and Zarrik, O and El Agouri, H and Fokar, M and Aghlallou, Y and El Jaoudi, R and Belyamani, L and Elkhannoussi, B and Ibrahimi, A}, title = {Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues.}, journal = {Journal of personalized medicine}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/jpm13030450}, pmid = {36983633}, issn = {2075-4426}, abstract = {Breast cancer is one of the main global priorities in terms of public health. It remains the most frequent cancer in women and is the leading cause of their death. The human microbiome plays various roles in maintaining health by ensuring a dynamic balance with the host or in the appearance of various pathologies including breast cancer. In this study, we performed an analysis of bacterial signature differences between tumor and adjacent tissues of breast cancer patients in Morocco. Using 16S rRNA gene sequencing, we observed that adjacent tissue contained a much higher percentage of the Gammaproteobacteria class (35.7%) while tumor tissue was characterized by a higher percentage of Bacilli and Actinobacteria classes, with about 18.8% and 17.2% average abundance, respectively. Analysis of tumor subtype revealed enrichment of genus Sphingomonodas in TNBC while Sphingomonodas was predominant in HER2. The LEfSe and the genus level heatmap analysis revealed a higher abundance of the Rothia genus in tumor tissues. The identified microbial communities can therefore serve as potential biomarkers for prognosis and diagnosis, while also helping to develop new strategies for the treatment of breast cancer patients.}, }
@article {pmid36982690, year = {2023}, author = {Belalov, IS and Sokolov, AA and Letarov, AV}, title = {Diversity-Generating Retroelements in Prokaryotic Immunity.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065614}, pmid = {36982690}, issn = {1422-0067}, abstract = {Adaptive immunity systems found in different organisms fall into two major types. Prokaryotes possess CRISPR-Cas systems that recognize former invaders using memorized (captured) pieces of their DNA as pathogen signatures. Mammals possess a vast repertoire of antibodies and T-cell receptor variants generated in advance. In this second type of adaptive immunity, a pathogen presentation to the immune system specifically activates the cells that express matching antibodies or receptors. These cells proliferate to fight the infection and form the immune memory. The principle of preemptive production of diverse defense proteins for future use can hypothetically take place in microbes too. We propose a hypothesis that prokaryotes employ diversity-generating retroelements to prepare defense proteins against yet-unknown invaders. In this study, we test this hypothesis with the methods of bioinformatics and identify several candidate defense systems based on diversity-generating retroelements.}, }
@article {pmid36982303, year = {2023}, author = {Giuffrè, M and Moretti, R and Tiribelli, C}, title = {Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, doi = {10.3390/ijms24065229}, pmid = {36982303}, issn = {1422-0067}, abstract = {The human gut microbiome plays a crucial role in human health and has been a focus of increasing research in recent years. Omics-based methods, such as metagenomics, metatranscriptomics, and metabolomics, are commonly used to study the gut microbiome because they provide high-throughput and high-resolution data. The vast amount of data generated by these methods has led to the development of computational methods for data processing and analysis, with machine learning becoming a powerful and widely used tool in this field. Despite the promising results of machine learning-based approaches for analyzing the association between microbiota and disease, there are several unmet challenges. Small sample sizes, disproportionate label distribution, inconsistent experimental protocols, or a lack of access to relevant metadata can all contribute to a lack of reproducibility and translational application into everyday clinical practice. These pitfalls can lead to false models, resulting in misinterpretation biases for microbe-disease correlations. Recent efforts to address these challenges include the construction of human gut microbiota data repositories, improved data transparency guidelines, and more accessible machine learning frameworks; implementation of these efforts has facilitated a shift in the field from observational association studies to experimental causal inference and clinical intervention.}, }
@article {pmid36981070, year = {2023}, author = {Zhang, T and Yue, Y and Jeong, SJ and Ryu, MS and Wu, X and Yang, HJ and Li, C and Jeong, DY and Park, S}, title = {Improvement of Estrogen Deficiency Symptoms by the Intake of Long-Term Fermented Soybeans (Doenjang) Rich in Bacillus Species through Modulating Gut Microbiota in Estrogen-Deficient Rats.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/foods12061143}, pmid = {36981070}, issn = {2304-8158}, abstract = {Traditionally made doenjang (TMD) produced by the long-term fermentation of soybeans with salt may improve symptoms of estrogen deficiency. We aimed to evaluate the effects of four TMD types, containing low and high amounts of Bacillus species and biogenic amines (HBHA, HBLA, LBHA, and LBLA), on energy, glucose, and lipid metabolism, by altering the gut microbiota in estrogen-deficient ovariectomized (OVX) rats. Their mechanisms were also examined. The OVX rats were divided into the control, cooked soybean (CSB), HBHA, LBHA, HBLA, and LBLA groups. Sham-operated rats were the normal control group. Serum 17β-estradiol concentrations were similar among all OVX groups. Tail skin temperatures, which are indicative of hot flashes, were higher in the control than the HBHA and HBLA groups and were similar to the normal control group. Weight gain and visceral fat mass were lower in the TMD and CSB intake groups but not as low as in the normal control group. Lean body mass showed a trend opposite to that of visceral fat in the respective groups. The hepatic triglyceride content decreased with the TMD intake compared to the control and CSB groups. mRNA expressions of the peroxisome proliferator-activated receptor-γ (PPAR-γ) and carnitine palmitoyltransferase-1 in the TMD and CSB groups were as high as in the normal control group, and the PPAR-γ mRNA expression was more elevated in the HBLA group than in the normal control group. The morphology of the intestines improved in the TMD groups compared to the control, and the HBHA and HBLA groups showed an enhanced improvement compared to the CSB group. The HBHA, HBLA, and LBHA groups increased the α-diversity of the cecal microbiota compared to the control. Akkermenia and Lactobacillus were higher in the HBLA and LBLA groups compared to the control. The expression of the estrogen, forkhead box proteins of the class-O subgroup, and insulin-signaling pathways were lower in the control group, and HBHA and HBLA prevented their decrement. In conclusion, long-term treatment with TMD containing high amounts of Bacillus potentially improves estrogen deficiency symptoms more than unfermented soybeans.}, }
@article {pmid36980929, year = {2023}, author = {Baeza, JA and Barata, R and Rajapakse, D and Penaloza, J and Harrison, P and Haberski, A}, title = {Mitochondrial Genomes Assembled from Non-Invasive eDNA Metagenomic Scat Samples in Critically Endangered Mammals.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/genes14030657}, pmid = {36980929}, issn = {2073-4425}, abstract = {The abundance of many large-bodied vertebrates, both in marine and terrestrial environments, has declined substantially due to global and regional climate stressors that define the Anthropocene. The development of genetic tools that can serve to monitor population's health non-intrusively and inform strategies for the recovery of these species is crucial. In this study, we formally evaluate whether whole mitochondrial genomes can be assembled from environmental DNA (eDNA) metagenomics scat samples. Mitogenomes of four different large vertebrates, the panda bear (Ailuropoda melanoleuca), the moon bear (Ursus thibetanus), the Java pangolin (Manis javanica), and the the North Atlantic right whale (Eubalaena glacialis) were assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 12x to 480x in 14 out of 18 different eDNA samples. Partial mitochondrial genomes were retrieved from three other eDNA samples. The complete mitochondrial genomes of the studied species were AT-rich and comprised 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative D-loop/control region. Synteny observed in all assembled mitogenomes was identical to that reported for specimens of the same and other closely related species. This study demonstrates that it is possible to assemble accurate whole mitochondrial chromosomes from eDNA samples (scats) using forthright bench and bioinformatics workflows. The retrieval of mitochondrial genomes from eDNA samples represents a tool to support bioprospecting, bio-monitoring, and other non-intrusive conservation strategies in species considered 'vulnerable', 'endangered', and/or 'critically endangered' by the IUCN Red List of Threatened Species.}, }
@article {pmid36980906, year = {2023}, author = {Das, R and Rai, A and Mishra, DC}, title = {CNN_FunBar: Advanced Learning Technique for Fungi ITS Region Classification.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/genes14030634}, pmid = {36980906}, issn = {2073-4425}, abstract = {Fungal species identification from metagenomic data is a highly challenging task. Internal Transcribed Spacer (ITS) region is a potential DNA marker for fungi taxonomy prediction. Computational approaches, especially deep learning algorithms, are highly efficient for better pattern recognition and classification of large datasets compared to in silico techniques such as BLAST and machine learning methods. Here in this study, we present CNN_FunBar, a convolutional neural network-based approach for the classification of fungi ITS sequences from UNITE+INSDC reference datasets. Effects of convolution kernel size, filter numbers, k-mer size, degree of diversity and category-wise frequency of ITS sequences on classification performances of CNN models have been assessed at all taxonomic levels (species, genus, family, order, class and phylum). It is observed that CNN models can produce >93% average accuracy for classifying ITS sequences from balanced datasets with 500 sequences per category and 6-mer frequency features at all levels. The comparative study has revealed that CNN_FunBar can outperform machine learning-based algorithms (SVM, KNN, Naïve-Bayes and Random Forest) as well as existing fungal taxonomy prediction software (funbarRF, Mothur, RDP Classifier and SINTAX). The present study will be helpful for fungal taxonomy classification using large metagenomic datasets.}, }
@article {pmid36979819, year = {2023}, author = {Leitao Filho, FS and Monica Peters, C and Sheel, AW and Yang, J and Nislow, C and Lam, S and Leung, JM and Sin, DD}, title = {Characterization of the Lower Airways and Oral Microbiota in Healthy Young Persons in the Community.}, journal = {Biomedicines}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/biomedicines11030841}, pmid = {36979819}, issn = {2227-9059}, abstract = {Lower airway dysbiosis contributes to disease pathogenesis in respiratory diseases. However, little is known regarding the microbiota of lower airways or the oral cavity of healthy young persons. To address this gap, 25 healthy persons (24.3 ± 3.3 years; 52% females; no current smokers) underwent bronchoscopy during which bronchial brushing (BB) and bronchoalveolar lavage (BAL) fluid were collected. Prior to the procedure, an oral wash (OW) sample was also obtained. Microbiome analyses (16S rRNA locus) were performed (alpha- and beta-diversity, taxa annotations, and predicted functional metagenomic profiles) according to the airway compartment (BB, BAL, and OW). The greatest microbial richness was observed in OW and the lowest in BB (p < 0.001). Microbial communities differed significantly across compartments (p < 0.001), especially between BB and OW. Taxa analyses showed a significantly higher abundance of Firmicutes (BB: 32.7%; BAL: 31.4%) compared to OW (20.9%) (p < 0.001). Conversely, Proteobacteria predominated in OW (27.9%) as opposed to BB (7.0%) and BAL (12.5%) (p < 0.001), mostly due to a greater abundance of the bacteria in the Haemophilus genus in the OW (p < 0.001). The lower airway microbiota (BB and BAL) is significantly different from the OW microbiota in healthy young persons with respect to microbial diversity, taxa profiles, and predicted function.}, }
@article {pmid36979806, year = {2023}, author = {Athanasopoulou, K and Adamopoulos, PG and Scorilas, A}, title = {Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics.}, journal = {Biomedicines}, volume = {11}, number = {3}, pages = {}, doi = {10.3390/biomedicines11030827}, pmid = {36979806}, issn = {2227-9059}, abstract = {Over 10[14] symbiotic microorganisms are present in a healthy human body and are responsible for the synthesis of vital vitamins and amino acids, mediating cellular pathways and supporting immunity. However, the deregulation of microbial dynamics can provoke diverse human diseases such as diabetes, human cancers, cardiovascular diseases, and neurological disorders. The human gastrointestinal tract constitutes a hospitable environment in which a plethora of microbes, including diverse species of archaea, bacteria, fungi, and microeukaryotes as well as viruses, inhabit. In particular, the gut microbiome is the largest microbiome community in the human body and has drawn for decades the attention of scientists for its significance in medical microbiology. Revolutions in sequencing techniques, including 16S rRNA and ITS amplicon sequencing and whole genome sequencing, facilitate the detection of microbiomes and have opened new vistas in the study of human microbiota. Especially, the flourishing fields of metagenomics and metatranscriptomics aim to detect all genomes and transcriptomes that are retrieved from environmental and human samples. The present review highlights the complexity of the gastrointestinal tract microbiome and deciphers its implication not only in cellular homeostasis but also in human diseases. Finally, a thorough description of the widely used microbiome detection methods is discussed.}, }
@article {pmid36979367, year = {2023}, author = {Saxena, A and Mathur, N and Pathak, P and Tiwari, P and Mathur, SK}, title = {Machine Learning Model Based on Insulin Resistance Metagenes Underpins Genetic Basis of Type 2 Diabetes.}, journal = {Biomolecules}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/biom13030432}, pmid = {36979367}, issn = {2218-273X}, abstract = {Insulin resistance (IR) is considered the precursor and the key pathophysiological mechanism of type 2 diabetes (T2D) and metabolic syndrome (MetS). However, the pathways that IR shares with T2D are not clearly understood. Meta-analysis of multiple DNA microarray datasets could provide a robust set of metagenes identified across multiple studies. These metagenes would likely include a subset of genes (key metagenes) shared by both IR and T2D, and possibly responsible for the transition between them. In this study, we attempted to find these key metagenes using a feature selection method, LASSO, and then used the expression profiles of these genes to train five machine learning models: LASSO, SVM, XGBoost, Random Forest, and ANN. Among them, ANN performed well, with an area under the curve (AUC) > 95%. It also demonstrated fairly good performance in differentiating diabetics from normal glucose tolerant (NGT) persons in the test dataset, with 73% accuracy across 64 human adipose tissue samples. Furthermore, these core metagenes were also enriched in diabetes-associated terms and were found in previous genome-wide association studies of T2D and its associated glycemic traits HOMA-IR and HOMA-B. Therefore, this metagenome deserves further investigation with regard to the cardinal molecular pathological defects/pathways underlying both IR and T2D.}, }
@article {pmid36978958, year = {2023}, author = {Lauritano, C and Montuori, E and De Falco, G and Carrella, S}, title = {In Silico Methodologies to Improve Antioxidants' Characterization from Marine Organisms.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antiox12030710}, pmid = {36978958}, issn = {2076-3921}, abstract = {Marine organisms have been reported to be valuable sources of bioactive molecules that have found applications in different industrial fields. From organism sampling to the identification and bioactivity characterization of a specific compound, different steps are necessary, which are time- and cost-consuming. Thanks to the advent of the -omic era, numerous genome, metagenome, transcriptome, metatranscriptome, proteome and microbiome data have been reported and deposited in public databases. These advancements have been fundamental for the development of in silico strategies for basic and applied research. In silico studies represent a convenient and efficient approach to the bioactivity prediction of known and newly identified marine molecules, reducing the time and costs of "wet-lab" experiments. This review focuses on in silico approaches applied to bioactive molecule discoveries from marine organisms. When available, validation studies reporting a bioactivity assay to confirm the presence of an antioxidant molecule or enzyme are reported, as well. Overall, this review suggests that in silico approaches can offer a valuable alternative to most expensive approaches and proposes them as a little explored field in which to invest.}, }
@article {pmid36978337, year = {2023}, author = {Rovira, P}, title = {Short-Term Impact of Oxytetracycline Administration on the Fecal Microbiome, Resistome and Virulome of Grazing Cattle.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/antibiotics12030470}, pmid = {36978337}, issn = {2079-6382}, abstract = {Antimicrobial resistance (AMR) is an important public health concern around the world. Limited information exists about AMR in grasslands-based systems where antibiotics are seldom used in beef cattle. The present study investigated the impacts of oxytetracycline (OTC) on the microbiome, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in grazing steers with no previous exposure to antibiotic treatments. Four steers were injected with a single dose of OTC (TREAT), and four steers were kept as control (CONT). The effects of OTC on fecal microbiome, ARGs, and VFGs were assessed for 14 days using 16S rRNA sequencing and shotgun metagenomics. Alpha and beta microbiome diversities were significantly affected by OTC. Following treatment, less than 8% of bacterial genera had differential abundance between CONT and TREAT samples. Seven ARGs conferring resistance to tetracycline (tet32, tet40, tet44, tetO, tetQ, tetW, and tetW/N/W) increased their abundance in the post-TREAT samples compared to CONT samples. In addition, OTC use was associated with the enrichment of macrolide and lincosamide ARGs (mel and lnuC, respectively). The use of OTC had no significant effect on VFGs. In conclusion, OTC induced short-term alterations of the fecal microbiome and enrichment of ARGs in the feces of grazing beef cattle.}, }
@article {pmid36977970, year = {2023}, author = {Amin, DH and Nageeb, WM and Elkelish, A and Makharita, RR}, title = {Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {36977970}, issn = {1678-4405}, abstract = {Pathogens resistant to antimicrobials form a significant threat to public health worldwide. Tackling multidrug-resistant pathogens via screening metagenomic libraries has become a common approach for the discovery of new antibiotics from uncultured microorganisms. This study focuses on capturing nonribosomal peptide synthase (NRPS) gene clusters implicated in the synthesis of many natural compounds of industrial relevance. A NRPS PCR assay was used to screen 2976 Escherichia coli clones in a soil metagenomic library to target NRPS genes. DNA extracts from 4 clones were sequenced and subjected to bioinformatic analysis to identify NRPS domains, their phylogeny, and substrate specificity.Successfully, 17 NRPS-positive hits with a biosynthetic potential were identified. DNA sequencing and BLAST analysis confirmed that NRPS protein sequences shared similarities with members of the genus Delftia in the Proteobacteria taxonomic position. Multiple alignment and phylogenetic analysis demonstrated that clones no. 15cd35 and 15cd37 shared low bootstrap values (54%) and were distantly far from close phylogenetic neighbors. Additionally, NRPS domain substrate specificity has no hits with the known ones; hence, they are more likely to use different substrates to produce new diverse antimicrobials. Further analysis confirmed that the NRPS hits resemble several transposon elements from other bacterial taxa, confirming its diversity. We confirmed that the analyses of the soil metagenomic library revealed a diverse set of NRPS related to the genus Delftia. An in-depth understanding of those positive NRPS hits is a crucial step for genetic manipulation of NRPS, shedding light on alternative novel antimicrobial compounds that can be used in drug discovery and hence supports the pharmaceutical sector.}, }
@article {pmid36977954, year = {2023}, author = {Mahiddine, FY and You, I and Park, H and Kim, MJ}, title = {Management of dog sperm parameters and gut microbiota composition with Lactobacillus rhamnosus supplementation.}, journal = {Veterinary research communications}, volume = {}, number = {}, pages = {}, pmid = {36977954}, issn = {1573-7446}, abstract = {The effects of probiotics supplementation on the reproductive function have been evaluated in many species, but no study has evaluated the changes in the gut microbiome along with the sperm quality changes simultaneously. This study evaluated the effects of dietary supplementation with probiotics on the gut microbiome, sperm quality and gene expression, along with possible correlations between these parameters in dogs. The dogs were supplemented with Lactobacillus rhamnosus for six weeks, and fecal and semen samples were collected at 0, 3, and 6 weeks. Fecal samples were assessed using 16S Metagenomic Sequencing for gut microbiome analysis; and semen samples were analyzed using computer-assisted sperm analysis, DNA and acrosome integrity assessment, viability and morphology assessment, and real-time PCR. The analyses suggested that probiotic supplementation improved kinematic parameters, viability, DNA and acrosome integrity, and morphology of sperms. The mRNA levels of genes associated with fertility, DNA repair and integrity, and antioxidation were also upregulated. The sperm parameters were positively correlated with the relative abundance of Actinobacteria, Allobaculum, Phascolarctobacterium and Catenibacterium, and negatively correlated with Faecalibacterium and Streptococcus. Taken together, the sperm quality enhancement through the gut-testis axis may be due to a change in the gut microorganisms populations.}, }
@article {pmid36977254, year = {2023}, author = {Becker, AAMJ and Munden, S and McCabe, E and Hurley, D and Fanning, S and Chapwanya, A and Butaye, P}, title = {The Endometrial Microbiota-16S rRNA Gene Sequence Signatures in Healthy, Pregnant and Endometritis Dairy Cows.}, journal = {Veterinary sciences}, volume = {10}, number = {3}, pages = {}, doi = {10.3390/vetsci10030215}, pmid = {36977254}, issn = {2306-7381}, abstract = {Endometritis is one of the most important causes of infertility in dairy cows, resulting in high economic losses in the dairy industry. Though the presence of a commensal uterine microbiota is now well established, the complex role of these bacteria in genital health, fertility, and susceptibility to uterine diseases remains unclear. In this study, we explore the endometrial microbiota through 16S rRNA gene profiling from cytobrush samples taken ex vivo from healthy, pregnant, and endometritis cows. There were no significant differences between healthy and pregnant cows, whose uterine microbiota were dominated by Streptococcus, Pseudomonas, Fusobacterium, Lactococcus and Bacteroides. Compared to pregnant and clinically healthy cows, the uterine bacterial community of endometritis cows was significantly decreased in species diversity (p < 0.05), reflecting uneven community composition in different patterns with either dominance of Escherichia-Shigella, Histophilus, Bacteroides and Porphyromonas or Actinobacteria.}, }
@article {pmid36976417, year = {2023}, author = {Zhou, Q and Yu, J and Song, X and Zhang, J and Zhang, B}, title = {The discovery of novel papillomaviruses in cats in Southwest China.}, journal = {Virus genes}, volume = {}, number = {}, pages = {1-5}, pmid = {36976417}, issn = {1572-994X}, abstract = {Feline viral diarrhea is a significant cause of death in kittens. In this study, 12 mammalian viruses were identified by metagenomic sequencing in diarrheal feces in 2019, 2020, and 2021, respectively. Interestingly, a novel of felis catus papillomavirus (FcaPV) was identified for the first time in China. Subsequently, we investigated the prevalence of FcaPV in 252 feline samples, including 168 diarrheal feces and 84 oral swabs, with a total of 57 (22.62%, 57/252) samples detected positive. Of the 57 positive samples, FcaPV genotype 3 (FcaPV-3) was detected at high prevalence rate (68.42%, 39/57), followed by FcaPV-4 (22.8%, 13/57), FcaPV-2 (17.54%, 10/57), and FcaPV-1 (1.75%, 1/55), while no FcaPV-5 and FcaPV-6. In addition, two novel putative FcaPVs were identified, which were the highest similarity to Lambdapillomavirus from Leopardus wiedii or canis familiaris, respectively. Therefore, this study was the first characterization of the viral diversity in feline diarrheal feces and the prevalence of FcaPV in Southwest China.}, }
@article {pmid36976214, year = {2023}, author = {Elvheim, AI and Li, C and Landfald, B}, title = {Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates.}, journal = {Marine drugs}, volume = {21}, number = {3}, pages = {}, doi = {10.3390/md21030165}, pmid = {36976214}, issn = {1660-3397}, abstract = {Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2-850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources.}, }
@article {pmid36975940, year = {2023}, author = {Manee, MM and Alqahtani, FH and Al-Shomrani, BM and El-Shafie, HAF and Dias, GB}, title = {Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest.}, journal = {Insects}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/insects14030255}, pmid = {36975940}, issn = {2075-4450}, abstract = {The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of palm trees worldwide. Mitigation of the economic and biodiversity impact it causes is an international priority that could be greatly aided by a better understanding of its biology and genetics. Despite its relevance, the biology of the RPW remains poorly understood, and research on management strategies often focuses on outdated empirical methods that produce sub-optimal results. With the development of omics approaches in genetic research, new avenues for pest control are becoming increasingly feasible. For example, genetic engineering approaches become available once a species's target genes are well characterized in terms of their sequence, but also population variability, epistatic interactions, and more. In the last few years alone, there have been major advances in omics studies of the RPW. Multiple draft genomes are currently available, along with short and long-read transcriptomes, and metagenomes, which have facilitated the identification of genes of interest to the RPW scientific community. This review describes omics approaches previously applied to RPW research, highlights findings that could be impactful for pest management, and emphasizes future opportunities and challenges in this area of research.}, }
@article {pmid36975833, year = {2023}, author = {Xiao, X and Luo, M and Zhang, C and Zhang, T and Yin, X and Wu, X and Zhao, J and Tao, J and Chen, Z and Liang, Q and Dong, X}, title = {Metal-Driven Anaerobic Oxidation of Methane as an Important Methane Sink in Methanic Cold Seep Sediments.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0533722}, doi = {10.1128/spectrum.05337-22}, pmid = {36975833}, issn = {2165-0497}, abstract = {Anaerobic oxidation of methane (AOM) coupled with reduction of metal oxides is supposed to be a globally important bioprocess in marine sediments. However, the responsible microorganisms and their contributions to methane budget are not clear in deep sea cold seep sediments. Here, we combined geochemistry, muti-omics, and numerical modeling to study metal-dependent AOM in methanic cold seep sediments in the northern continental slope of the South China Sea. Geochemical data based on methane concentrations, carbon stable isotope, solid-phase sediment analysis, and pore water measurements indicate the occurrence of anaerobic methane oxidation coupled to metal oxides reduction in the methanic zone. The 16S rRNA gene and transcript amplicons, along with metagenomic and metatranscriptomic data suggest that diverse anaerobic methanotrophic archaea (ANME) groups actively mediated methane oxidation in the methanic zone either independently or in syntrophy with, e.g., ETH-SRB1, as potential metal reducers. Modeling results suggest that the estimated rates of methane consumption via Fe-AOM and Mn-AOM were both 0.3 μmol cm[-2] year[-1], which account for ~3% of total CH4 removal in sediments. Overall, our results highlight metal-driven anaerobic oxidation of methane as an important methane sink in methanic cold seep sediments. IMPORTANCE Anaerobic oxidation of methane (AOM) coupled with reduction of metal oxides is supposed to be a globally important bioprocess in marine sediments. However, the responsible microorganisms and their contributions to methane budget are not clear in deep sea cold seep sediments. Our findings provide a comprehensive view of metal-dependent AOM in the methanic cold seep sediments and uncovered the potential mechanisms for involved microorganisms. High amounts of buried reactive Fe(III)/Mn(IV) minerals could be an important available electron acceptors for AOM. It is estimated that metal-AOM at least contributes 3% of total methane consumption from methanic sediments to the seep. Therefore, this research paper advances our understanding of the role of metal reduction to the global carbon cycle, especially the methane sink.}, }
@article {pmid36975809, year = {2023}, author = {Falardeau, J and Yildiz, E and Yan, Y and Castellarin, SD and Wang, S}, title = {Microbiome and Physicochemical Features Associated with Differential Listeria monocytogenes Growth in Soft, Surface-Ripened Cheeses.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0200422}, doi = {10.1128/aem.02004-22}, pmid = {36975809}, issn = {1098-5336}, abstract = {Soft-ripened cheeses (SRCs) are at a higher risk for the growth of the foodborne pathogen Listeria monocytogenes due to favorable moisture content and pH compared to other cheeses. L. monocytogenes growth is not consistent across SRCs, however, and may be affected by physicochemical and/or microbiome characteristics of the cheeses. Therefore, the purpose of this study was to investigate how the physicochemical and microbiome profiles of SRCs may affect L. monocytogenes growth. Forty-three SRCs produced from raw (n = 12) or pasteurized (n = 31) milk were inoculated with L. monocytogenes (10[3] CFU/g), and the pathogen growth was monitored over 12 days at 8°C. In parallel, the pH, water activity (aw), microbial plate counts, and organic acid content of cheeses were measured, and the taxonomic profiles of the cheese microbiomes were measured using 16S rRNA gene targeted amplicon sequencing and shotgun metagenomic sequencing. L. monocytogenes growth differed significantly between cheeses (analysis of variance [ANOVA]; P < 0.001), with increases ranging from 0 to 5.4 log CFU (mean of 2.5 ± 1.2 log CFU), and was negatively correlated with aw. Raw milk cheeses showed significantly lower L. monocytogenes growth than pasteurized-milk cheeses (t test; P = 0.008), possibly due to an increase in microbial competition. L. monocytogenes growth in cheeses was positively correlated with the relative abundance of Streptococcus thermophilus (Spearman correlation; P < 0.0001) and negatively correlated with the relative abundances of Brevibacterium aurantiacum (Spearman correlation; P = 0.0002) and two Lactococcus spp. (Spearman correlation; P < 0.01). These results suggest that the cheese microbiome may influence the food safety in SRCs. IMPORTANCE Previous studies have identified differences in L. monocytogenes growth between SRCs, but no clear mechanism has yet been elucidated. To the best of our knowledge, this is the first study to collect a wide range of SRCs from retail sources and attempt to identify key factors associated with pathogen growth. A key finding in this research was the positive correlation between the relative abundance of S. thermophilus and the growth of L. monocytogenes. The inclusion of S. thermophilus as a starter culture is more common in industrialized SRC production, suggesting that industrial production of SRC may increase the risk of L. monocytogenes growth. Overall, the results of this study further our understanding of the impact of aw and the cheese microbiome on the growth of L. monocytogenes in SRCs, hopefully leading toward the development of SRC starter/ripening cultures that can prevent L. monocytogenes growth.}, }
@article {pmid36975807, year = {2023}, author = {Zhang, W and Liu, Y and Zheng, K and Xing, J and Li, Q and Gu, C and Wang, Z and Shao, H and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Wong, LL and Liang, Y and McMinn, A and Wang, M}, title = {Discovery of an Abundant Viral Genus in Polar Regions through the Isolation and Genomic Characterization of a New Virus against Oceanospirillaceae.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0189622}, doi = {10.1128/aem.01896-22}, pmid = {36975807}, issn = {1098-5336}, abstract = {The marine bacterial family Oceanospirillaceae, is well-known for its ability to degrade hydrocarbons and for its close association with algal blooms. However, only a few Oceanospirillaceae-infecting phages have been reported thus far. Here, we report on a novel Oceanospirillum phage, namely, vB_OsaM_PD0307, which has a 44,421 bp linear dsDNA genome and is the first myovirus infecting Oceanospirillaceae. A genomic analysis demonstrated that vB_OsaM_PD0307 is a variant of current phage isolates from the NCBI data set but that it has similar genomic features to two high-quality, uncultured viral genomes identified from marine metagenomes. Hence, we propose that vB_OsaM_PD0307 can be classified as the type phage of a new genus, designated Oceanospimyovirus. Additionally, metagenomic read mapping results have further shown that Oceanospimyovirus species are widespread in the global ocean, display distinct biogeographic distributions, and are abundant in polar regions. In summary, our findings expand the current understanding of the genomic characteristics, phylogenetic diversity, and distribution of Oceanospimyovirus phages. IMPORTANCE Oceanospirillum phage vB_OsaM_PD0307 is the first myovirus found to infect Oceanospirillaceae, and it represents a novel abundant viral genus in polar regions. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral genus, namely Oceanospimyovirus.}, }
@article {pmid36975801, year = {2023}, author = {Carter, KA and Fodor, AA and Balkus, JE and Zhang, A and Serrano, MG and Buck, GA and Engel, SM and Wu, MC and Sun, S}, title = {Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0100322}, doi = {10.1128/msystems.01003-22}, pmid = {36975801}, issn = {2379-5077}, abstract = {Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome. Findings from other body sites cannot easily be generalized to the vaginal microbiome due to unique features of vaginal microbial ecology, and investigators seeking to use metagenome inference in vaginal microbiome research are "flying blind" with respect to potential bias these methods may introduce into analyses. We compared the performance of PICRUSt2 and Tax4Fun2 using paired 16S rRNA gene amplicon sequencing and whole-metagenome sequencing data from vaginal samples from 72 pregnant individuals enrolled in the Pregnancy, Infection, and Nutrition (PIN) cohort. Participants were selected from those with known birth outcomes and adequate 16S rRNA gene amplicon sequencing data in a case-control design. Cases experienced early preterm birth (<32 weeks of gestation), and controls experienced term birth (37 to 41 weeks of gestation). PICRUSt2 and Tax4Fun2 performed modestly overall (median Spearman correlation coefficients between observed and predicted KEGG ortholog [KO] relative abundances of 0.20 and 0.22, respectively). Both methods performed best among Lactobacillus crispatus-dominated vaginal microbiotas (median Spearman correlation coefficients of 0.24 and 0.25, respectively) and worst among Lactobacillus iners-dominated microbiotas (median Spearman correlation coefficients of 0.06 and 0.11, respectively). The same pattern was observed when evaluating correlations between univariable hypothesis test P values generated with observed and predicted metagenome data. Differential metagenome inference performance across vaginal microbiota community types can be considered differential measurement error, which often causes differential misclassification. As such, metagenome inference will introduce hard-to-predict bias (toward or away from the null) in vaginal microbiome research. IMPORTANCE Compared to taxonomic composition, the functional potential within a bacterial community is more relevant to establishing mechanistic understandings and causal relationships between the microbiome and health outcomes. Metagenome inference attempts to bridge the gap between 16S rRNA gene amplicon sequencing and whole-metagenome sequencing by predicting a microbiome's gene content based on its taxonomic composition and annotated genome sequences of its members. Metagenome inference methods have been evaluated primarily among gut samples, where they appear to perform fairly well. Here, we show that metagenome inference performance is markedly worse for the vaginal microbiome and that performance varies across common vaginal microbiome community types. Because these community types are associated with sexual and reproductive outcomes, differential metagenome inference performance will bias vaginal microbiome studies, obscuring relationships of interest. Results from such studies should be interpreted with substantial caution and the understanding that they may over- or underestimate associations with metagenome content.}, }
@article {pmid36975791, year = {2023}, author = {Mejia, ME and Robertson, CM and Patras, KA}, title = {Interspecies Interactions within the Host: the Social Network of Group B Streptococcus.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0044022}, doi = {10.1128/iai.00440-22}, pmid = {36975791}, issn = {1098-5522}, abstract = {Group B Streptococcus (GBS) is a pervasive neonatal pathogen accounting for a combined half a million deaths and stillbirths annually. The most common source of fetal or neonatal GBS exposure is the maternal microbiota. GBS asymptomatically colonizes the gastrointestinal and vaginal mucosa of 1 in 5 individuals globally, although its precise role in these niches is not well understood. To prevent vertical transmission, broad-spectrum antibiotics are administered to GBS-positive mothers during labor in many countries. Although antibiotics have significantly reduced GBS early-onset neonatal disease, there are several unintended consequences, including an altered neonatal microbiota and increased risk for other microbial infections. Additionally, the incidence of late-onset GBS neonatal disease remains unaffected and has sparked an emerging hypothesis that GBS-microbe interactions in developing neonatal gut microbiota may be directly involved in this disease process. This review summarizes our current understanding of GBS interactions with other resident microbes at the mucosal surface from multiple angles, including clinical association studies, agriculture and aquaculture observations, and experimental animal model systems. We also include a comprehensive review of in vitro findings of GBS interactions with other bacterial and fungal microbes, both commensal and pathogenic, along with newly established animal models of GBS vaginal colonization and in utero or neonatal infection. Finally, we provide a perspective on emerging areas of research and current strategies to design microbe-targeting prebiotic or probiotic therapeutic intervention strategies to prevent GBS disease in vulnerable populations.}, }
@article {pmid36974462, year = {2023}, author = {Zhang, S and Li, S and Huang, J and Ding, X and Qiu, Y and Luo, X and Meng, J and Hu, Y and Zhou, H and Fan, H and Cao, Y and Gao, F and Xue, Y and Zou, M}, title = {Gram-negative bacteria and lipopolysaccharides as risk factors for the occurrence of diabetic foot.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1210/clinem/dgad178}, pmid = {36974462}, issn = {1945-7197}, abstract = {CONTEXT: Imbalance of the skin microbial community could impair skin immune homeostasis and thus trigger skin lesions. Dysbiosis of skin microbiome may be involved in the early pathogenesis of diabetic foot (DF). However, the potential mechanism remains unclear.<br><br>OBJECTIVE: To investigate the dynamic composition and function of the foot skin microbiome with risk stratification for DF and assess whether dysbiosis of the skin microbiome induces diabetic skin lesions.<br><br>METHODS: We enrolled 90 consecutive subjects who were divided into five groups based on DF risk stratification: very low, low, moderate and high risk for ulcers and a healthy control group. Integrated analysis of 16S rRNA and metagenomic sequencing of cotton swab samples was applied to identify the foot skin microbiome composition and functions in subjects. Then, a mouse model of microbiota transplantation was used to evaluate the effects of the skin microbiome on diabetic skin lesions.<br><br>RESULTS: The results demonstrated that, with the progression of diabetic complications, the proportion of gram-negative bacteria in plantar skin increased. At the species level, metagenome sequencing analyses showed Moraxella osloensis to be a representative core strain in the high-risk group. The major microbial metabolites affecting diabetic skin lesions were increased amino acid metabolites, and antibiotic resistance genes in microorganisms were abundant. Skin microbiota from high-risk patients induced more inflammatory cell infiltration, similar to the lipopolysaccharide (LPS)-stimulated response, which was inhibited by Toll-like receptor 4 (TLR4) antagonists.<br><br>CONCLUSIONS: The skin microbiome in patients with diabetes undergoes dynamic changes at taxonomic and functional levels with the progression of diabetic complications. The increase in gram-negative bacteria on the skin surface through LPS-TLR4 signal transduction could induce inflammatory response in early diabetic skin lesions.}, }
@article {pmid36973750, year = {2023}, author = {Rivarez, MPS and Pecman, A and Bačnik, K and Maksimović, O and Vučurović, A and Seljak, G and Mehle, N and Gutiérrez-Aguirre, I and Ravnikar, M and Kutnjak, D}, title = {In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {60}, pmid = {36973750}, issn = {2049-2618}, abstract = {BACKGROUND: In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data.<br><br>RESULTS: Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments.<br><br>CONCLUSIONS: We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies. Video Abstract.}, }
@article {pmid36973710, year = {2023}, author = {Li, H and Wang, H and Ju, H and Lv, J and Yang, S and Zhang, W and Lu, H}, title = {Comparison of gut viral communities in children under 5 years old and newborns.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {52}, pmid = {36973710}, issn = {1743-422X}, abstract = {OBJECTIVES: The gut virome of humans is mainly composed of bacteriophages and their role in shaping the gut microbiome and influencing human health is increasingly recognized. However, little is known about the dynamic changes of the gut virome in children and its role in growth and development. In this study, we collected fecal samples from newborns and children under 5 years old from the same area during the same time period to investigate the gut viral community using viral metagenomic technique.<br><br>METHODS: We used viral metagenomics to compare the gut bacteriophage composition between newborns and children under 5 years of age. We collected fecal samples from 45 newborns who were born at the Affiliated Hospital of Jiangsu University and 45 healthy children who were examined at the same hospital. The two groups were classified as the newborn group and the children group.<br><br>RESULTS: Our sequencing analysis showed that the number of seqeunce reads of the children group were more than that of the newborn group. The results of alpha diversity and beta diversity both indicated that the diversity of the children group was significantly higher than that of the newborn group and the children group is different from the newborn group. The abundance of gut virome in the children group was also higher than that in the newborn group. The analysis of the genetic characteristics of the viruses showed that the phage genome was scattered and clustered with specificity.<br><br>CONCLUSION: Our findings indicate that the gut bacteriophage communities undergo changes over time, presenting diversity and dynamic characteristics. We characterized the composition of gut virome in children and newborns in this region. However, further research is needed to investigate the function of bacteriophages in the ecology of the gastrointestinal tract.}, }
@article {pmid36973336, year = {2023}, author = {Rodríguez-Gijón, A and Buck, M and Andersson, AF and Izabel-Shen, D and Nascimento, FJA and Garcia, SL}, title = {Linking prokaryotic genome size variation to metabolic potential and environment.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {25}, pmid = {36973336}, issn = {2730-6151}, abstract = {While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.}, }
@article {pmid36972958, year = {2023}, author = {Muzny, CA and Van Gerwen, OT and Schroeder, JA and Kay-Duncan, ES and Siwakoti, K and Aaron, KJ and Eastlund, IC and Graves, KJ and Elnaggar, JH and Tamhane, A and Long, D and Van Wagoner, N and Toh, E and Taylor, CM}, title = {Impact of testosterone use on the vaginal microbiota of transgender men, including susceptibility to bacterial vaginosis: study protocol for a prospective, observational study.}, journal = {BMJ open}, volume = {13}, number = {3}, pages = {e073068}, doi = {10.1136/bmjopen-2023-073068}, pmid = {36972958}, issn = {2044-6055}, abstract = {INTRODUCTION: The effect of testosterone (T) therapy on the vaginal microbiota of transgender men (TGM) is not well characterised, although one cross-sectional study comparing the vaginal microbiota of cisgender women to TGM on T≥1 year found that, in 71% of the TGM, the vaginal microbiota was less likely to be Lactobacillus-dominated and more likely to be enriched with >30 other bacterial species, many associated with bacterial vaginosis (BV). This prospective study aims to investigate changes in the composition of the vaginal microbiota over time in TGM who retain their natal genitalia (ie, vagina) and initiate T. In addition, we will identify changes in the vaginal microbiota preceding incident BV (iBV) in this cohort while investigating behavioural factors, along with hormonal shifts, which may be associated with iBV.<br><br>METHODS AND ANALYSIS: T-na&#xef;ve TGM who have not undergone gender-affirming genital surgery with normal baseline vaginal microbiota (ie, no Amsel criteria, normal Nugent Score with no Gardnerella vaginalis morphotypes) will self-collect daily vaginal specimens for 7&#x2009;days prior to initiating T and for 90 days thereafter. These specimens will be used for vaginal Gram stain, 16S rRNA gene sequencing and shotgun metagenomic sequencing to characterise shifts in the vaginal microbiota over time, including development of iBV. Participants will complete daily diaries on douching, menses and behavioural factors including sexual activity during the study.<br><br>ETHICS AND DISSEMINATION: This protocol is approved through the single Institutional Review Board mechanism by the University of Alabama at Birmingham. External relying sites are the Louisiana State University Health Sciences Center, New Orleans Human Research Protection Program and the Indiana University Human Research Protection Program. Study findings will be presented at scientific conferences and peer-reviewed journals as well as shared with community advisory boards at participating gender health clinics and community-based organisations servicing transgender people.<br><br>REGISTRATION DETAILS: Protocol # IRB-300008073.}, }
@article {pmid36805473, year = {2023}, author = {Jia, Y and Liu, ML and López-Pujol, J and Jia, RW and Kou, YX and Yue, M and Guan, TX and Li, ZH}, title = {The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis.}, journal = {Molecular phylogenetics and evolution}, volume = {182}, number = {}, pages = {107736}, doi = {10.1016/j.ympev.2023.107736}, pmid = {36805473}, issn = {1095-9513}, mesh = {*Apiaceae/genetics ; Bayes Theorem ; Ecosystem ; Metagenomics ; Phylogeny ; *Hybridization, Genetic ; }, abstract = {Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.}, }
@article {pmid36801373, year = {2023}, author = {Spaulding, F and McLaughlin, JF and Cheek, RG and McCracken, KG and Glenn, TC and Winker, K}, title = {Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex.}, journal = {Molecular phylogenetics and evolution}, volume = {182}, number = {}, pages = {107733}, doi = {10.1016/j.ympev.2023.107733}, pmid = {36801373}, issn = {1095-9513}, mesh = {Humans ; Animals ; *Ducks/genetics ; *Gene Flow ; Phylogeny ; Metagenomics ; DNA, Mitochondrial/genetics ; }, abstract = {The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspecies (Anas crecca crecca, A. c. nimia, and A. c. carolinensis) with a close relative, the yellow-billed teal (Anas flavirostris) from South America. A. c. crecca and A. c. carolinensis are seasonal migrants, while the other taxa are sedentary. We examined divergence and speciation patterns in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and genome-wide nuclear DNA obtained from 1,393 ultraconserved element (UCE) loci. Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca, A. c. nimia, and A. c. carolinensis clustering together to form one polytomous clade, with A. flavirostris sister to this clade. This relationship can be summarized as (crecca, nimia, carolinensis)(flavirostris). However, whole mitogenomes revealed a different phylogeny: (crecca, nimia)(carolinensis, flavirostris). The best demographic model for key pairwise comparisons supported divergence with gene flow as the probable speciation mechanism in all three contrasts (crecca-nimia, crecca-carolinensis, and carolinensis-flavirostris). Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris (M ∼0.1-0.4 individuals/generation), albeit low, was not expected. Three geographically oriented modes of divergence are likely involved in the diversification of this complex: heteropatric (crecca-nimia), parapatric (crecca-carolinensis), and (mostly) allopatric (carolinensis-flavirostris). Our study shows that ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems with historically uncertain relationships and species limits.}, }
@article {pmid36972812, year = {2023}, author = {Tian, H and Li, Y and Chen, H and Zhang, J and Hui, M and Xu, X and Su, Q and Smets, BF}, title = {Aerobic biodegradation of quinoline under denitrifying conditions in membrane-aerated biofilm reactor.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {121507}, doi = {10.1016/j.envpol.2023.121507}, pmid = {36972812}, issn = {1873-6424}, abstract = {Aerobic denitrification is being investigated as a novel biological nitrogen removal process, yet the knowledge on aerobic denitrification is limited to pure culture isolations and its occurrence in bioreactors remains unclear. This study investigated the feasibility and capacity of applying aerobic denitrification in membrane aerated biofilm reactor (MABR) for biological treatment of quinoline-laden wastewater. Stable and efficient removals of quinoline (91.5 ± 5.2%) and nitrate (NO3[-]) (86.5 ± 9.3%) were obtained under different operational conditions. Enhanced formation and function of extracellular polymeric substances (EPS) were observed at increasing quinoline loadings. MABR biofilm was highly enriched with aerobic quinoline-degrading bacteria, with a predominance of Rhodococcus (26.9 ± 3.7%) and secondary abundance of Pseudomonas (1.7 ± 1.2%) and Comamonas (0.94 ± 0.9%). Metagenomic analysis indicated that Rhodococcus contributed significantly to both aromatic degradation (24.5 ± 21.3%) and NO3[-] reduction (4.5 ± 3.9%), indicating its key role in aerobic denitrifying quinoline biodegradation. At increasing quinoline loadings, abundances of aerobic quinoline degradation gene oxoO and denitrifying genes of napA, nirS and nirK increased; there was a significant positive correlation of oxoO with nirS and nirK (p < 0.05). Aerobic quinoline degradation was likely initiated by hydroxylation, encoded by oxoO, followed by stepwise oxidations through 5,6-dihydroxy-1H-2-oxoquinoline or 8-hydroxycoumarin pathway. The results advance our understanding of quinoline degradation during biological nitrogen removal, and highlight the potential implementation of aerobic denitrification driven quinoline biodegradation in MABR for simultaneous removal of nitrogen and recalcitrant organic carbon from coking, coal gasification and pharmaceutical wastewaters.}, }
@article {pmid36972309, year = {2023}, author = {Krishnan, S and DeMaere, MZ and Beck, D and Ostrowski, M and Seymour, JR and Darling, AE}, title = {Rhometa: Population recombination rate estimation from metagenomic read datasets.}, journal = {PLoS genetics}, volume = {19}, number = {3}, pages = {e1010683}, doi = {10.1371/journal.pgen.1010683}, pmid = {36972309}, issn = {1553-7404}, abstract = {Prokaryotic evolution is influenced by the exchange of genetic information between species through a process referred to as recombination. The rate of recombination is a useful measure for the adaptive capacity of a prokaryotic population. We introduce Rhometa (https://github.com/sid-krish/Rhometa), a new software package to determine recombination rates from shotgun sequencing reads of metagenomes. It extends the composite likelihood approach for population recombination rate estimation and enables the analysis of modern short-read datasets. We evaluated Rhometa over a broad range of sequencing depths and complexities, using simulated and real experimental short-read data aligned to external reference genomes. Rhometa offers a comprehensive solution for determining population recombination rates from contemporary metagenomic read datasets. Rhometa extends the capabilities of conventional sequence-based composite likelihood population recombination rate estimators to include modern aligned metagenomic read datasets with diverse sequencing depths, thereby enabling the effective application of these techniques and their high accuracy rates to the field of metagenomics. Using simulated datasets, we show that our method performs well, with its accuracy improving with increasing numbers of genomes. Rhometa was validated on a real S. pneumoniae transformation experiment, where we show that it obtains plausible estimates of the rate of recombination. Finally, the program was also run on ocean surface water metagenomic datasets, through which we demonstrate that the program works on uncultured metagenomic datasets.}, }
@article {pmid36971593, year = {2023}, author = {Liu, F and Lu, H and Dong, B and Huang, X and Cheng, H and Qu, R and Hu, Y and Zhong, L and Guo, Z and You, Y and Xu, ZZ}, title = {Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/- Bacteria.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0073822}, doi = {10.1128/msystems.00738-22}, pmid = {36971593}, issn = {2379-5077}, abstract = {PMA (propidium monoazide) is one of the few methods that are compatible with metagenomic sequencing to characterize the live/intact microbiota. However, its efficiency in complex communities such as saliva and feces is still controversial. An effective method for depleting host and dead bacterial DNA in human microbiome samples is lacking. Here, we systematically evaluate the efficiency of osmotic lysis and PMAxx treatment (lyPMAxx) in characterizing the viable microbiome with four live/dead Gram+/Gram- microbial strains in simple synthetic and spiked-in complex communities. We show that lyPMAxx-quantitative PCR (qPCR)/sequencing eliminated more than 95% of the host and heat-killed microbial DNA and had a much smaller effect on the live microbes in both simple mock and spiked-in complex communities. The overall microbial load and the alpha diversity of the salivary and fecal microbiome were decreased by lyPMAxx, and the relative abundances of the microbes were changed. The relative abundances of Actinobacteria, Fusobacteria, and Firmicutes in saliva were decreased by lyPMAxx, as was that of Firmicutes in feces. We also found that the frequently used sample storage method, freezing with glycerol, killed or injured 65% and 94% of the living microbial cells in saliva and feces, respectively, with the Proteobacteria phylum affected most in saliva and the Bacteroidetes and Firmicutes phyla affected most in feces. By comparing the absolute abundance variation of the shared species among different sample types and individuals, we found that sample habitat and personal differences affected the response of microbial species to lyPMAxx and freezing. IMPORTANCE The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes. PMA-qPCR was used to characterize the viable microbes in previous studies. However, its efficiency in complex communities such as saliva and feces is still controversial. By spiking-in four live/dead Gram+/Gram- bacterial strains, we demonstrate that lyPMAxx can effectively discriminate between live and dead microbes in the simple synthetic community and complex human microbial communities (saliva and feces). In addition, freezing storage was found to kill or injure the microbes in saliva and feces significantly, as measured with lyPMAxx-qPCR/sequencing. This method has a promising prospect in the viable/intact microbiota detection of complex human microbial communities.}, }
@article {pmid36971577, year = {2023}, author = {Balière, C and Hourdel, V and Kwasiborski, A and Grassin, Q and Feher, M and Hoinard, D and Vanhomwegen, J and Taieb, F and Consigny, PH and Manuguerra, JC and Leclercq, I and Batéjat, C and Caro, V}, title = {Complete Genome Sequences of Monkeypox Virus from a French Clinical Sample and the Corresponding Isolated Strain, Obtained Using Nanopore Sequencing.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0000923}, doi = {10.1128/mra.00009-23}, pmid = {36971577}, issn = {2576-098X}, abstract = {We report the whole-genome sequences of a monkeypox virus from the skin lesion of a French patient and the corresponding isolated viral strain. Both viral genomic sequences were successfully obtained by applying shotgun metagenomics using the Oxford Nanopore Technologies sequencing approach.}, }
@article {pmid36971547, year = {2023}, author = {Etienne-Mesmin, L and Meslier, V and Uriot, O and Fournier, E and Deschamps, C and Denis, S and David, A and Jegou, S and Morabito, C and Quinquis, B and Thirion, F and Plaza Oñate, F and Le Chatelier, E and Ehrlich, SD and Blanquet-Diot, S and Almeida, M}, title = {In Vitro Modelling of Oral Microbial Invasion in the Human Colon.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0434422}, doi = {10.1128/spectrum.04344-22}, pmid = {36971547}, issn = {2165-0497}, abstract = {Recent advances in the human microbiome characterization have revealed significant oral microbial detection in stools of dysbiotic patients. However, little is known about the potential interactions of these invasive oral microorganisms with commensal intestinal microbiota and the host. In this proof-of-concept study, we proposed a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Oral invasion of the intestinal microbiota was simulated by injection of enriched saliva in the in vitro colon model inoculated with a fecal sample from the same healthy adult donor. The mucosal compartment of M-ARCOL was able to retain the highest species richness levels over time, while species richness levels decreased in the luminal compartment. This study also showed that oral microorganisms preferably colonized the mucosal microenvironment, suggesting potential oral-to-intestinal mucosal competitions. This new model of oral-to-gut invasion can provide useful mechanistic insights into the role of oral microbiome in various disease processes. IMPORTANCE Here, we propose a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Our study revealed the importance of integrating the mucus compartment, which retained higher microbial richness during fermentation, showed the preference of oral microbial invaders for the mucosal resources, and indicated potential oral-to-intestinal mucosal competitions. It also underlined promising opportunities to further understand mechanisms of oral invasion into the human gut microbiome, define microbe-microbe and mucus-microbe interactions in a compartmentalized fashion, and help to better characterize the potential of oral microbial invasion and their persistence in the gut.}, }
@article {pmid36970947, year = {2023}, author = {Ermolenko, E and Sitkin, S and Vakhitov, T and Solovyeva, O and Karaseva, A and Morozova, A and Kotyleva, M and Shumikhina, I and Lavrenova, N and Demyanova, E and Dmitriev, A and Suvorov, A}, title = {Evaluation of the effectiveness of personalised therapy for the patients with irritable bowel syndrome.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-12}, doi = {10.3920/BM2022.0053}, pmid = {36970947}, issn = {1876-2891}, abstract = {Intestinal microbiota correction in the therapy of irritable bowel syndrome (IBS) is an important medical problem. We conducted a laboratory and pilot clinical trial to investigate the effect of autoprobiotic bacteria, indigenous bifidobacteria and enterococci isolated from faeces and grown on artificial media to use as personified food additives in IBS treatment. Convincing evidence of the clinical efficacy of autoprobiotic was demonstrated by the disappearance of dyspeptic symptoms. The microbiome of patients with IBS was compared to a group of healthy volunteers and changes in the microbiome after autoprobiotic use were detected by quantitative polymerase chain reaction and 16S rRNA metagenome analysis. The possibility of reducing opportunistic microorganisms in the treatment of IBS with autoprobiotics has been convincingly proven. The quantitative content of enterococci in the intestinal microbiota was higher in IBS patients than in healthy volunteers and increased after therapy. An increase in the relative abundance of genera Coprococcus, Blautia and a decrease in the relative abundance of Paraprevotella spp. were found at the end of therapy. A metabolome study which was performed by gas chromatography and mass spectrometry demonstrated an increase in the content of oxalic acid, a decrease of dodecanoate, lauric acid, and other metabolome components after taking autoprobiotics. Some of these parameters correlated with the relative abundances of Paraprevotella spp., Enterococcus spp., and Coprococcus spp. representative of the microbiome. Apparently, they reflected the peculiarities of metabolic compensation and changes in the microbiota. Therefore, the use of autoprobiotics for treatment of IBS may lead to a stable positive clinical effect, associated with compensatory changes in the intestinal microbiota, and accompanied by corresponding changes in metabolic processes in the organism.}, }
@article {pmid36970703, year = {2023}, author = {Pan, J and Zeng, M and Zhao, M and Huang, L}, title = {Research Progress on the detection methods of porcine reproductive and respiratory syndrome virus.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1097905}, pmid = {36970703}, issn = {1664-302X}, abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) causes clinical syndromes typified as reproductive disorders in sows and respiratory diseases in piglets. PRRSV remains one of the most prevalent pathogens affecting the pig industry, because of its complex infection profile and highly heterogeneous genetic and recombination characteristics. Therefore, a rapid and effective PRRSV detection method is important for the prevention and control of PRRS. With extensive in-depth research on PRRSV detection methods, many detection methods have been improved and promoted. Laboratory methods include techniques based on virus isolation (VI), enzyme-linked immunosorbent assays (ELISA), indirect immunofluorescence assays (IFA), immunoperoxidase monolayer assays (IPMA), polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), digital PCR (dPCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), clustered regularly interspaced short palindromic repeats (CRISPR), metagenomic next-generation sequencing (mNGS), and other methods. This study reviews the latest research on improving the main PRRSV detection methods and discusses their advantages and disadvantages.}, }
@article {pmid36970696, year = {2023}, author = {Dai, R and Wu, H and Liu, G and Shen, L and Geng, Y and Zhang, S and Zhou, H and Jiang, C and Gong, J and Fan, X and Ji, C}, title = {Investigation of bacterial and fungal population structure on environmental surfaces of three medical institutions during the COVID-19 pandemic.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1089474}, pmid = {36970696}, issn = {1664-302X}, abstract = {OBJECTIVES: To evaluate the population structure of environmental bacteria and fungi in three different types of medical institutions and the potential risks due to antibiotic resistance during the coronavirus disease 2019 (COVID-19) pandemic.<br><br>METHODS: One hundred twenty-six environmental surface samples were collected from three medical institutions during the COVID-19 pandemic. A total of 6,093 and 13,514 representative sequences of 16S and ITS ribosomal RNA (rRNA) were obtained by amplicon sequencing analysis. The functional prediction was performed using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States tool based on the Greengenes database and the FAPROTAX database.<br><br>RESULTS: On environmental surfaces in three medical institutions during the COVID-19 pandemic, Firmicutes (51.6%) and Bacteroidetes (25%) were the dominant bacteria, while Ascomycota (39.4%) and Basidiomycota (14.2%) were the dominant fungi. A number of potential bacterial and fungal pathogens were successfully identified by the metagenomic approach. Furthermore, compared with the bacterial results, the fungi showed a generally closer Bray Curtis distance between samples. The overall ratio of Gram-negative bacteria to Gram-positive bacteria was about 3:7. The proportion of stress-tolerant bacteria in medical institutions A, B and C reached 88.9, 93.0 and 93.8%, respectively. Anaerobic bacteria accounted for 39.6% in outdoor environments, 77.7% in public areas, 87.9% in inpatient areas and 79.6% in restricted areas. Finally, the &#x3b2;-Lactam resistance pathway and polymyxin resistance pathway were revealed through functional prediction.<br><br>CONCLUSION: We described the microbial population structure changes in three different types of medical institutions using the metagenomic approach during the COVID-19 pandemic. We found that the disinfection measures performed by three healthcare facilities may be effective on the "ESKAPE" pathogens, but less effective on fungal pathogens. Moreover, emphasis should be given to the prevention and control of &#x3b2;-lactam and polymyxin antibiotics resistance bacteria during the COVID-19 pandemic.}, }
@article {pmid36970681, year = {2023}, author = {Guo, K and Li, J and Li, X and Huang, J and Zhou, Z}, title = {Emerging trends and focus on the link between gut microbiota and type 1 diabetes: A bibliometric and visualization analysis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1137595}, pmid = {36970681}, issn = {1664-302X}, abstract = {OBJECTIVE: To conduct the first thorough bibliometric analysis to evaluate and quantify global research regarding to the gut microbiota and type 1 diabetes (T1D).<br><br>METHODS: A literature search for research studies on gut microbiota and T1D was conducted using the Web of Science Core Collection (WoSCC) database on 24 September 2022. VOSviewer software and the packages Bibliometrix R and ggplot used in RStudio were applied to perform the bibliometric and visualization analysis.<br><br>RESULTS: A total of 639 publications was extracted using the terms "gut microbiota" and "type 1 diabetes" (and their synonyms in MeSH). Ultimately, 324 articles were included in the bibliometric analysis. The United States and European countries are the main contributors to this field, and the top 10 most influential institutions are all based in the United States, Finland and Denmark. The three most influential researchers in this field are Li Wen, Jorma Ilonen and Mikael Knip. Historical direct citation analysis showed the evolution of the most cited papers in the field of T1D and gut microbiota. Clustering analysis defined seven clusters, covering the current main topics in both basic and clinical research on T1D and gut microbiota. The most commonly found high-frequency keywords in the period from 2018 to 2021 were "metagenomics," "neutrophils" and "machine learning."<br><br>CONCLUSION: The application of multi-omics and machine learning approaches will be a necessary future step for better understanding gut microbiota in T1D. Finally, the future outlook for customized therapy toward reshaping gut microbiota of T1D patients remains promising.}, }
@article {pmid36970670, year = {2023}, author = {Seyler, LM and Kraus, EA and McLean, C and Spear, JR and Templeton, AS and Schrenk, MO}, title = {An untargeted exometabolomics approach to characterize dissolved organic matter in groundwater of the Samail Ophiolite.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1093372}, pmid = {36970670}, issn = {1664-302X}, abstract = {The process of serpentinization supports life on Earth and gives rise to the habitability of other worlds in our Solar System. While numerous studies have provided clues to the survival strategies of microbial communities in serpentinizing environments on the modern Earth, characterizing microbial activity in such environments remains challenging due to low biomass and extreme conditions. Here, we used an untargeted metabolomics approach to characterize dissolved organic matter in groundwater in the Samail Ophiolite, the largest and best characterized example of actively serpentinizing uplifted ocean crust and mantle. We found that dissolved organic matter composition is strongly correlated with both fluid type and microbial community composition, and that the fluids that were most influenced by serpentinization contained the greatest number of unique compounds, none of which could be identified using the current metabolite databases. Using metabolomics in conjunction with metagenomic data, we detected numerous products and intermediates of microbial metabolic processes and identified potential biosignatures of microbial activity, including pigments, porphyrins, quinones, fatty acids, and metabolites involved in methanogenesis. Metabolomics techniques like the ones used in this study may be used to further our understanding of life in serpentinizing environments, and aid in the identification of biosignatures that can be used to search for life in serpentinizing systems on other worlds.}, }
@article {pmid36970663, year = {2023}, author = {Zhong, X and Zhao, Y and Huang, L and Liu, J and Wang, K and Gao, X and Zhao, X and Wang, X}, title = {Remodeling of the gut microbiome by Lactobacillus johnsonii alleviates the development of acute myocardial infarction.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1140498}, pmid = {36970663}, issn = {1664-302X}, abstract = {INTRODUCTION: The gut microbial community, which can be disturbed or repaired by changes in the internal environment, contributes to the development of acute myocardial infarction (AMI). Gut probiotics play a role in microbiome remodeling and nutritional intervention post-AMI. A newly isolated Lactobacillus johnsonii strain EU03 has shown potential as a probiotic. Here, we investigated the cardioprotective function and mechanism of L. johnsonii through gut microbiome remodeling in AMI rats.<br><br>METHODS: A rat model of left anterior descending coronary artery ligation (LAD)-mediated AMI was assessed with echocardiography, histology, and serum cardiac biomarkers to evaluate the beneficial effects of L. johnsonii. The immunofluorescence analysis was utilized to visualize the intestinal barrier changes. Antibiotic administration model was used for assessing the gut commensals' function in the improvement of cardiac function post-AMI. The underlying beneficial mechanism through L. johnsonii enrichment was further investigated by metagenomics and metabolomics analysis.<br><br>RESULTS: A 28-day treatment with L. johnsonii protected cardiac function, delayed cardiac pathology, suppressed myocardial injury cytokines, and improved gut barrier integrity. The microbiome composition was reprogrammed by enhancing the abundance of L. johnsonii. Microbiome dysbiosis by antibiotics abrogated the improvement of cardiac function post-AMI by L. johnsonii. L. johnsonii enrichment caused remodeling of gut microbiome by increasing the abundance of Muribaculaceae, Lactobacillus, and decreasing Romboutsia, Clostridia UCG-014, which were correlated with cardiac traits and serum metabolic biomarkers 16,16-dimethyl-PGA2, and Lithocholate 3-O-glucuronide.<br><br>CONCLUSION: These findings reveal that gut microbiome remodeling by L. johnsonii ameliorates the cardiac function post-AMI and might advance microbiome-targeted nutritional intervention.Graphical Abstract.}, }
@article {pmid36970502, year = {2023}, author = {Liu, B and Warnow, T}, title = {WITCH-NG: efficient and accurate alignment of datasets with sequence length heterogeneity.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad024}, pmid = {36970502}, issn = {2635-0041}, abstract = {SUMMARY: Multiple sequence alignment is a basic part of many bioinformatics pipelines, including in phylogeny estimation, prediction of structure for both RNAs and proteins, and metagenomic sequence analysis. Yet many sequence datasets exhibit substantial sequence length heterogeneity, both because of large insertions and deletions in the evolutionary history of the sequences and the inclusion of unassembled reads or incompletely assembled sequences in the input. A few methods have been developed that can be highly accurate in aligning datasets with sequence length heterogeneity, with UPP one of the first methods to achieve good accuracy, and WITCH a recent improvement on UPP for accuracy. In this article, we show how we can speed up WITCH. Our improvement includes replacing a critical step in WITCH (currently performed using a heuristic search) by a polynomial time exact algorithm using Smith-Waterman. Our new method, WITCH-NG (i.e. 'next generation WITCH') achieves the same accuracy but is substantially faster. WITCH-NG is available at https://github.com/RuneBlaze/WITCH-NG.<br><br>The datasets used in this study are from prior publications and are freely available in public repositories, as indicated in the Supplementary Materials.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.}, }
@article {pmid36970243, year = {2023}, author = {Wang, L and Lin, C and Qi, Y}, title = {Gestational psittacosis causes severe pneumonia and miscarriage: A case report and literature review.}, journal = {Radiology case reports}, volume = {18}, number = {5}, pages = {1959-1962}, pmid = {36970243}, issn = {1930-0433}, abstract = {Psittacosis is an uncommon zoonotic illness, and gestational psittacosis is even rarer. The clinical signs and symptoms of psittacosis are varied, often overlooked, and swiftly identified by metagenomic next-generation sequencing. We recorded the case of a 41-year-old pregnant woman with psittacosis where the disease was not detected early on, resulting in severe pneumonia and fetal miscarriage. The clinical symptoms, diagnosis, and treatment of psittacosis in pregnancy are the subject of this case study.}, }
@article {pmid36969214, year = {2023}, author = {Feng, R and Zhu, Q and Li, Q and Zhai, Y and Wang, J and Qin, C and Liang, D and Zhang, R and Tian, H and Liu, H and Chen, Y and Fu, Y and Wang, X and Ding, X}, title = {Microbiota-ear-brain interaction is associated with generalized anxiety disorder through activation of inflammatory cytokine responses.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1117726}, pmid = {36969214}, issn = {1664-3224}, abstract = {INTRODUCTION: Generalized anxiety disorder (GAD) is one of the most enduring anxiety disorders, being associated with increased systemic inflammation. However, the trigger and mechanisms underlying the activation of inflammatory cytokine responses in GAD remain poorly understood.<br><br>MATERIALS AND METHODS: We characterized the ear canal microbiome in GAD patients through 16S rRNA gene sequencing and metagenomic sequencing and identified the serum inflammatory markers in GAD patients. Spearman correlations were applied to test the relationship between the microbiota changes and systemic inflammation.<br><br>RESULTS: Our findings showed the higher microbial diversity, accompanied with the significantly increased abundance of Proteobacteria, and decreased abundance of Firmicutes in the ear canal of GAD participants compared to that of the age- and sex-matched healthy controls (HC). Metagenomic sequencing showed that Pseudomonas aeruginosa were significantly increased at species-level in GAD patients. Furthermore, we observed the relative abundance of Pseudomonas aeruginosa was positively associated with elevated systemic inflammatory markers and the severity of disease, suggesting that these ear canal microbiota alterations might be correlated with GAD by activating the inflammatory response.<br><br>CONCLUSIONS: These findings indicate that microbiota-ear-brain interaction via upregulating inflammatory reaction involve in the development of GAD, as well as suggest that ear canal bacterial communities may be a target for therapeutic intervention.}, }
@article {pmid36968950, year = {2023}, author = {Brochu, E and Huletsky, A and Boudreau, DK and Raymond, F and Bérubé, &#xc8; and Ouameur, AA and Frenette, J and Boissinot, M and Corbeil, J and Bergeron, MG}, title = {Characterization of vancomycin-resistance vanD gene clusters in the human intestinal microbiota by metagenomics and culture-enriched metagenomics.}, journal = {JAC-antimicrobial resistance}, volume = {5}, number = {2}, pages = {dlad026}, pmid = {36968950}, issn = {2632-1823}, abstract = {OBJECTIVES: To characterize vancomycin-resistance vanD gene clusters and potential vanD-carrying bacteria in the intestinal microbiota of healthy volunteers exposed or not to β-lactam antibiotics.<br><br>METHODS: Stool samples were collected before and after 7 days of cefprozil &#x3b2;-lactam antibiotic exposure of 18 participants and six control participants who were not exposed to the antibiotic at the same time points. Metagenomic sequencing and culture-enriched metagenomic sequencing (with and without &#x3b2;-lactam selection) were used to characterize vanD gene clusters and determine potential vanD-carrying bacteria. Alteration by antimicrobials was also examined.<br><br>RESULTS: Culture enrichment allowed detection of vanD genes in a large number of participants (11/24; 46%) compared to direct metagenomics (2/24; 8%). vanD genes were detected in stool cultures only following &#x3b2;-lactam exposure, either after &#x3b2;-lactam treatment of participants or after culture of stools with &#x3b2;-lactam selection. Six types of vanD gene clusters were identified. Two types of vanD cluster highly similar to those of enterococci were found in two participants. Other vanD genes or vanD clusters were nearly identical to those identified in commensal anaerobic bacteria of the families Lachnospiraceae and Oscillospiraceae and/or bordered by genomic sequences similar or related to these anaerobes, suggesting that they are the origin or carriers of vanD.<br><br>CONCLUSIONS: This study showed that culture-enriched metagenomics allowed detection of vanD genes not detected by direct metagenomics and revealed collateral enrichment of bacteria containing vancomycin-resistance vanD genes following exposure to &#x3b2;-lactams, with a higher prevalence of the most likely gut commensal anaerobes carrying vanD. These commensal anaerobes could be the reservoir of vanD genes carried by enterococci.}, }
@article {pmid36968356, year = {2023}, author = {Zhang, M and Xiao, N and Yang, H and Li, Y and Gao, F and Li, J and Zhang, Z}, title = {The layout measures of micro-sprinkler irrigation under plastic film regulate tomato soil bacterial community and root system.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1136439}, pmid = {36968356}, issn = {1664-462X}, abstract = {INTRODUCTION: The change in rhizosphere soil bacterial community and root system under new water-saving device is not clear.<br><br>METHODS: A completely randomized experimental design was used to explore the effects of different micropore group spacing (L1: 30 cm micropore group spacing, L2: 50 cm micropore group spacing) and capillary arrangement density (C1: one pipe for one row, C2: one pipe for two rows, C3: one pipe for three rows) on tomato rhizosphere soil bacteria community, roots and tomato yield under MSPF. The bacteria in tomato rhizosphere soil were sequenced by 16S rRNA gene amplicon metagenomic sequencing technology, the interaction of bacterial community, root system and yield in tomato rhizosphere soil was quantitatively described based on regression analysis.<br><br>RESULTS: Results showed that L1 was not only beneficial to the development of tomato root morphology, but also promoted the ACE index of tomato soil bacterial community structure and the abundance of nitrogen and phosphorus metabolism functional genes. The yield and crop water use efficiency (WUE) of spring tomato and autumn tomato in L1 were about 14.15% and 11.27%, 12.64% and 10.35% higher than those in L2. With the decrease of capillary arrangement density, the diversity of bacterial community structure in tomato rhizosphere soil decreased, and the abundance of nitrogen and phosphorus metabolism functional genes of soil bacteria also decreased. The small abundance of soil bacterial functional genes limited the absorption of soil nutrients by tomato roots and roots morphological development. The yield and crop water use efficiency of spring and autumn tomato in C2 were significantly higher than those in C3 about 34.76% and 15.23%, 31.94% and 13.91%, respectively. The positive interaction between soil bacterial community and root morphological development of tomato was promoted by the capillary layout measures of MSPF.<br><br>DISCUSSION: The L1C2 treatment had a stable bacterial community structure and good root morphological development, which positively promoted the increase of tomato yield. The interaction between soil microorganisms and roots of tomato was regulated by optimizing the layout measures of MSPF to provide data support for water-saving and yield-increasing of tomato in Northwest China.}, }
@article {pmid36968018, year = {2023}, author = {Muñoz-Barrera, A and Ciuffreda, L and Alcoba-Florez, J and Rubio-Rodríguez, LA and Rodríguez-Pérez, H and Gil-Campesino, H and García-Martínez de Artola, D and Salas-Hernández, J and Rodríguez-Núñez, J and Íñigo-Campos, A and García-Olivares, V and Díez-Gil, O and González-Montelongo, R and Valenzuela-Fernández, A and Lorenzo-Salazar, JM and Flores, C}, title = {Bioinformatic approaches to draft the viral genome sequence of Canary Islands cases related to the multicountry mpox virus 2022-outbreak.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {2197-2203}, pmid = {36968018}, issn = {2001-0370}, abstract = {On July 23, 2022, monkeypox disease (mpox) was declared a Public Emergency of International Concern (PHEIC) by the World Health Organization (WHO) due to a multicountry outbreak. In Europe, several cases of mpox virus (MPXV) infection related to this outbreak were detected in the Canary Islands (Spain). Here we describe the combination of viral DNA sequencing and bioinformatic approaches, including methods for de novo genome assembly and short- and long-read technologies, used to reconstruct the first MPXV genome isolated in the Canary Islands on the 31st of May 2022 from a male adult patient with mild symptoms. The same sequencing and bioinformatic approaches were then validated with three other positive cases of MPXV infection from the same mpox outbreak. We obtained the best results using a reference-based approach with short reads, evidencing 46-79 nucleotide variants against viral sequences from the 2018-2019 mpox outbreak and placing the viral sequences in the new B.1 sublineage of clade IIb of the MPXV classification. This study of MPXV demonstrates the potential of metagenomics sequencing for rapid and precise pathogen identification.}, }
@article {pmid36967692, year = {2023}, author = {Niu, J and Kong, X and Li, Q and Zhang, Y and Yuan, J and Liu, J and Zhang, Y}, title = {Deciphering different effects of ZVI and NaOH on metabolic characteristics in the process of methanogenesis recovery from VFA suppression.}, journal = {Journal of environmental management}, volume = {336}, number = {}, pages = {117686}, doi = {10.1016/j.jenvman.2023.117686}, pmid = {36967692}, issn = {1095-8630}, abstract = {Dosing zero valent iron (ZVI) or sodium hydroxide (NaOH) is the common method of addressing acidification in anaerobic digestion (AD) systems; however, few studies have discussed and compared their effects on microbial metabolism. In the present study, microbial syntrophy and metabolic pathways under ZVI and NaOH regulation are comparatively analyzed through microbial network analysis and metagenomic/metaproteomic analyses. CH4 yield in the ZVI reactor was 414 mL/gVS, an increase of 23% when compared with that in the reactor with NaOH dosing (336 mL/gVS). The methanogenesis recovery period in the ZVI reactor (37 days) was shorter than that in the NaOH reactor (48 days). Co-occurrence networks indicated that ZVI promoted Methanoculleus and Methanosarcina to establish a complex syntrophic association with SAO bacteria (Syntrophaceticus and Aminobacterium) and syntrophic acetogens (Syntrophomonas), strengthening SAO-hydrogenotrophic methanogenesis (HM) and acetoclastic methanogenesis (AM) pathways simultaneously. Metagenomic analysis showed that the relative abundance of mcrA and fwdB in the ZVI reactor was higher 27% than that in the NaOH reactor. Furthermore, through metaproteomics analysis, much more enzymes related to glucose degradation, bioconversion of butyric acid and pyruvate, conversion of formate and acetate to CO2, and production of CH4 from acetate and CO2 were significantly upregulated under ZVI regulation than under NaOH regulation (fold change relative to control [FC] > 1.5, p < 0.05). The results of the present study enhance our understanding of methanogenic mechanisms under the regulation of ZVI, providing a theoretical basis for its practical application in AD systems experiencing VFA suppression.}, }
@article {pmid36967247, year = {2023}, author = {O'Connor, L and Heyderman, R}, title = {The challenges of defining the human nasopharyngeal resistome.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.02.008}, pmid = {36967247}, issn = {1878-4380}, abstract = {The nasopharynx is an important microbial reservoir for the emergence and spread of antibiotic-resistant organisms. The nasopharyngeal resistome is an extensive, adaptable reservoir of antibiotic-resistance genes (ARGs) within this niche. Metagenomic sequencing decodes the genetic material of all organisms within a sample using next-generation technologies, permitting unbiased discovery of novel ARGs and associated mobile genetic elements (MGEs). The challenges of sequencing a low-biomass bacterial sample have limited exploration of the nasopharyngeal resistome. Here, we explore the current understanding of the nasopharyngeal resistome, particularly the role of MGEs in propagating antimicrobial resistance (AMR), explore the advantages and limitations of metagenomic sequencing technologies and bioinformatic pipelines for nasopharyngeal resistome analysis, and highlight the key outstanding questions for future research.}, }
@article {pmid36967003, year = {2023}, author = {Li, J and Xu, X and Chen, C and Xu, L and Du, Z and Gu, L and Xiang, P and Shi, D and Huangfu, X and Liu, F}, title = {Conductive materials enhance microbial salt-tolerance in anaerobic digestion of food waste: Microbial response and metagenomics analysis.}, journal = {Environmental research}, volume = {}, number = {}, pages = {115779}, doi = {10.1016/j.envres.2023.115779}, pmid = {36967003}, issn = {1096-0953}, abstract = {Previous studies have shown that high salinity environments can inhibit anaerobic digestion (AD) of food waste (FW). Finding ways to alleviate salt inhibition is important for the disposal of the growing amount of FW. We selected three common conductive materials (powdered activated carbon, magnetite, and graphite) to understand their performance and individual mechanisms that relieve salinity inhibition. Digester performances and related enzyme parameters were compared. Our data revealed that under normal and low salinity stress conditions, the anaerobic digester ran steady without significant inhibitions. Further, the presence of conductive materials promoted conversion rate of methanogenesis. This promotion effect was highest from magnetite > powdered activated carbon (PAC) > graphite. At 1.5% salinity, PAC and magnetite are beneficial in maintaining high methane production efficiency while control and the graphite added digester acidified and failed rapidly. Additionally, metagenomics and binning were used to analyze the metabolic capacity of the microorganisms. Some species enriched by PAC and magnetite possessed higher cation transport capacities and were to accumulate compatible solutes. PAC and magnetite promoted direct interspecies electron transference (DIET) and syntrophic oxidation of butyrate and propionate. Also, the microorganisms had more energy available to cope with salt inhibition in the PAC and magnetite added digesters. Our data imply that the promotion of Na+/H+ antiporter, K+ uptake, and osmoprotectant synthesis or transport by conductive materials may be crucial for their proliferation in highly stressful environments. These findings will help to understand the mechanisms of alleviate salt inhibition by conductive materials and help to recover methane from high-salinity FW.}, }
@article {pmid36966989, year = {2023}, author = {Chen, Z and Song, B and Guo, H and Xia, D and Cai, Y and Wang, Y and Zhao, W}, title = {Metagenomic characterization of biomethane transformation by lipid-catalyzed anaerobic fermentation of lignite.}, journal = {Environmental research}, volume = {}, number = {}, pages = {115777}, doi = {10.1016/j.envres.2023.115777}, pmid = {36966989}, issn = {1096-0953}, abstract = {The present study aims at using lipid in a novel way to improve the efficiency of methane production from lignite anaerobic digestion. The obtained results showed an increase by 3.13 times of the cumulative biomethane content of lignite anaerobic fermentation, when 1.8 g lipid was added. The gene expression of functional metabolic enzymes was also found to be enhanced during the anaerobic fermentation. Moreover, the enzymes related to fatty acid degradation such as long-chain Acyl-CoA synthetase and Acyl-CoA dehydrogenase were increased by 1.72 and 10.48 times, respectively, which consequently, accelerated the conversion of fatty acid. Furthermore, the addition of lipid enhanced the carbon dioxide trophic and acetic acid trophic metabolic pathways. Hence, the addition of lipids was argued to promote the production of methane from lignite anaerobic fermentation, which provided a new insight for the conversion and utilization of lipid waste.}, }
@article {pmid36966826, year = {2023}, author = {Zhao, Z and Yu, C and Yang, C and Gao, B and Jiménez, N and Wang, C and Li, F and Ao, Y and Zheng, L and Huang, F and Tomberlin, JK and Ren, Z and Yu, Z and Zhang, J and Cai, M}, title = {Mitigation of antibiotic resistome in swine manure by black soldier fly larval conversion combined with composting.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163065}, doi = {10.1016/j.scitotenv.2023.163065}, pmid = {36966826}, issn = {1879-1026}, abstract = {The increasing prevalence of antibiotic resistance genes (ARGs) in animal manure has attracted considerable attention because of their potential contribution to the development of multidrug resistance worldwide. Insect technology may be a promising alternative for the rapid attenuation of ARGs in manure; however, the underlying mechanism remains unclear. This study aimed to evaluate the effects of black soldier fly (BSF, Hermetia illucens [L.]) larvae conversion combined with composting on ARGs dynamics in swine manure and to uncover the mechanisms through metagenomic analysis. Compared to natural composting (i.e. without BSF), BSFL conversion combined with composting reduced the absolute abundance of ARGs by 93.2 % within 28 days. The rapid degradation of antibiotics and nutrient reformulation during BSFL conversion combined with composting indirectly altered manure bacterial communities, resulting in a lower abundance and richness of ARGs. The number of main antibiotic-resistant bacteria (e.g., Prevotella, Ruminococcus) decreased by 74.9 %, while their potential antagonistic bacteria (e.g., Bacillus, Pseudomonas) increased by 128.7 %. The number of antibiotic-resistant pathogenic bacteria (e.g., Selenomonas, Paenalcaligenes) decreased by 88.3 %, and the average number of ARGs carried by each human pathogenic bacterial genus declined by 55.8 %. BSF larvae gut microbiota (e.g., Clostridium butyricum, C. bornimense) could help reduce the risk of multidrug-resistant pathogens. These results provide insight into a novel approach to mitigate multidrug resistance from the animal industry in the environment by using insect technology combined with composting, in particular in light of the global "One Health" requirements.}, }
@article {pmid36966821, year = {2023}, author = {Zhang, H and Gong, W and Xue, Y and Zeng, W and Wang, H and Wang, J and Tang, X and Li, G and Liang, H}, title = {Municipal wastewater contains antibiotic treatment using O2 transfer membrane based biofilm reactor: Interaction between regular pollutants metabolism and sulfamethoxazole degradation.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {163060}, doi = {10.1016/j.scitotenv.2023.163060}, pmid = {36966821}, issn = {1879-1026}, abstract = {The antibiotic sulfamethoxazole (SMX) is frequently detected in wastewater treatment plant effluents and has attracted significant attention owing to its significant potential environmental effects. We present a novel O2 transfer membrane based biofilm reactor (O2TM-BR) to treat municipal wastewater to eliminate containing SMX. Furthermore, conducting metagenomics analyses, the interactions in biodegradation process between SMX and regular pollutants (NH4[+]-N and COD) were studied. Results suggest that O2TM-BR yields evident advantages in SMX degradation. Increasing SMX concentrations did not affect the efficiency of the system, and the effluent concentration remained consistent at approximately 17.0 μg/L. The interaction experiment showed that heterotrophic bacteria tend to consume easily degradable COD for metabolism, resulting in a delay (>36 h) in complete SMX degradation, which is 3-times longer than without COD. It is worth noting that the taxonomic and functional structure and composition in nitrogen metabolism were significantly shifted upon the SMX. NH4[+]-N removal remained unaffected by SMX in O2TM-BR, and the expression of K10944 and K10535 has no significant difference under the stress of SMX (P > 0.02). However, the K00376 and K02567 required in the nitrate reductase is inhibited by SMX (P < 0.01), which hinders the reduction of NO3[-]-N and hence the accumulation of TN. This study provides a new method for SMX treatment and reveals the interaction between SMX and conventional pollutants in O2TM-BR as well as the microbial community function and assembly mechanism.}, }
@article {pmid36966280, year = {2023}, author = {Zhao, Y and Yi, J and Xiang, J and Jia, W and Chen, A and Chen, L and Zheng, L and Zhou, W and Wu, M and Yu, Z and Tang, J}, title = {Exploration of lung mycobiome in the patients with non-small-cell lung cancer.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {81}, pmid = {36966280}, issn = {1471-2180}, abstract = {As the Human Microbiome Project (HMP) progresses, the relationship between microbes and human health has been receiving increasing attention. A growing number of reports support the correlation between cancer and microbes. However, most studies have focused on bacteria, rather than fungal communities. In this study, we studied the alteration in lung mycobiome in patients with non-small-cell lung cancer (NSCLC) using metagenomic sequencing and qPCR. The higher fungal diversity and more complex network were observed in the patients with NSCLC. In addition, Alternaria arborescens was found as the most relevant fungus to NSCLC, and the enrichment of it in cancerous tissue was also detected. This study proposes that the changes in fungal communities may be closely related to lung cancer, and provides insights into further exploration the relationship between lung cancer and fungi.}, }
@article {pmid36966258, year = {2023}, author = {Deng, L and Li, Q and Hu, W and Chen, X and Chen, T and Song, S and Mo, P and Zou, S and Zhang, Y and Gao, S and Chen, L and Zhuang, K and Yang, R and Xiong, Y}, title = {Metagenomic next-generation sequencing versus traditional laboratory methods for the diagnosis of central nervous system opportunistic infections in HIV-infected Chinese adults.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4921}, pmid = {36966258}, issn = {2045-2322}, abstract = {To evaluate clinical value of metagenomic next-generation sequencing (mNGS) in people living with HIV/AIDS (PLWHA) who had CNS disorders. Cerebrospinal fluid (CSF) samples from 48 PLWHA presenting with CNS disorders were sequenced using mNGS and compared with clinical conventional diagnostic methods. In total, 36/48 ss(75%) patients were diagnosed with pathogen(s) infection by mNGS, and the positive detection proportion by mNGS was higher than that by clinical conventional diagnostic methods (75% vs 52.1%, X[2] = 5.441, P = 0.020). Thirteen out of 48 patients (27.1%) were detected with 3-7 pathogens by mNGS. Moreover, 77 pathogen strains were detected, of which 94.8% (73/77) by mNGS and 37.0% (30/77) by clinical conventional methods (X[2] = 54.206, P < 0.001). The sensitivity and specificity of pathogens detection by mNGS were 63.9% (23/36) and 66.7% (8/12), respectively, which were superior to that by clinical conventional methods (23/36 vs 9/25, X[2] = 4.601, P = 0.032; 8/12 vs 5/23, X[2] = 5.029, P = 0.009). The application of mNGS was superior for its ability to detect a variety of unknown pathogens and multiple pathogens infection, and relatively higher sensitivity and specificity in diagnosis of CNS disorders in PLWHA.}, }
@article {pmid36966231, year = {2023}, author = {Berglund, F and Ebmeyer, S and Kristiansson, E and Larsson, DGJ}, title = {Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {321}, pmid = {36966231}, issn = {2399-3642}, abstract = {The emergence and spread of mobile antibiotic resistance genes (ARGs) in pathogens have become a serious threat to global health. Still little is known about where ARGs gain mobility in the first place. Here, we aimed to collect evidence indicating where such initial mobilization events of clinically relevant ARGs may have occurred. We found that the majority of previously identified origin species did not carry the mobilizing elements that likely enabled intracellular mobility of the ARGs, suggesting a necessary interplay between different bacteria. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements. Most origin species were only occasionally detected in other environments. Co-occurrence of origin species and corresponding mobilizing elements were rare in human microbiota. Our results identify wastewaters and wastewater-impacted environments as plausible arenas for the initial mobilization of resistance genes.}, }
@article {pmid36966151, year = {2023}, author = {Lin, X and Hu, T and Chen, J and Liang, H and Zhou, J and Wu, Z and Ye, C and Jin, X and Xu, X and Zhang, W and Jing, X and Yang, T and Wang, J and Yang, H and Kristiansen, K and Xiao, L and Zou, Y}, title = {The genomic landscape of reference genomes of cultivated human gut bacteria.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1663}, pmid = {36966151}, issn = {2041-1723}, abstract = {Culture-independent metagenomic studies have revolutionized our understanding of the gut microbiota. However, the lack of full genomes from cultured species is still a limitation for in-depth studies of the gut microbiota. Here we present a substantially expanded version of our Cultivated Genome Reference (CGR), termed CGR2, providing 3324 high-quality draft genomes from isolates selected from a large-scale cultivation of bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (179 previously unidentified species) from 8 phyla, and uncovers a genomic and functional diversity of Collinsella aerofaciens. The CGR2 genomes match 126 metagenome-assembled genomes without cultured representatives in the Unified Human Gastrointestinal Genome (UHGG) collection and harbor 3767 unidentified secondary metabolite biosynthetic gene clusters, providing a source of natural compounds with pharmaceutical potentials. We uncover accurate phage-bacterium linkages providing information on the evolutionary characteristics of interaction between bacteriophages and bacteria at the strain level.}, }
@article {pmid36965360, year = {2023}, author = {Li, Z and Qing, Y and Cui, G and Li, M and Liu, T and Zeng, Y and Zhou, C and Hu, X and Jiang, J and Wang, D and Gao, Y and Zhang, J and Cai, C and Wang, T and Wan, C}, title = {Shotgun metagenomics reveals abnormal short-chain fatty acid-producing bacteria and glucose and lipid metabolism of the gut microbiota in patients with schizophrenia.}, journal = {Schizophrenia research}, volume = {255}, number = {}, pages = {59-66}, doi = {10.1016/j.schres.2023.03.005}, pmid = {36965360}, issn = {1573-2509}, abstract = {Evidence has shown that the gut microbiota is closely related to the pathogenesis of schizophrenia, but temporal changes in the gut microbiota of patients with schizophrenia (SZ) during treatment remain unclear. Here, to evaluate temporal changes in the gut microbiota in schizophrenia, we performed whole-genome shotgun metagenomics on fecal samples from 36 healthy controls (HCs) and 19 baseline-period patients, and followed up with patients upon treatment. Compared to that in HCs, beta diversity in SZ was significantly distinct. The genera Bacteroides, Prevotella and Clostridium were the top 3 altered genera between SZ and HCs, and the Bacteroides-Prevotella ratio was significantly increased in SZ. Thirty-three percent of differentially abundant species were short-chain fatty acid (SCFA)-producing bacteria. Functional analysis showed that glucose and lipid metabolism of the gut microbiota was decreased in SZ compared with those in HCs. The abundances of two rate-limiting enzymes in glucose and lipid metabolism, phosphofructokinase (PFK) and acetyl-CoA carboxylase (ACC), were significantly decreased in SZ, and differentially abundant metabolism-related enzymes were significantly associated with SCFA-producing bacteria. Next, we found that the abundance of SCFA-producing bacteria also changed after treatment and that Clostridium was significantly negatively correlated with the total positive and negative syndrome scale (PANSS) score in patients. Functional analysis showed that glycoside hydrolase family 30 incrementally increased in abundance during treatment and were significantly associated with SCFA-producing bacteria. Our findings help to provide evidence for the role of gut microbiota in the occurrence and development of schizophrenia.}, }
@article {pmid36965294, year = {2023}, author = {Hu, P and Qian, Y and Liu, J and Gao, L and Li, Y and Xu, Y and Wu, J and Hong, Y and Ford, T and Radian, A and Yang, Y and Gu, JD}, title = {Delineation of the complex microbial nitrogen-transformation network in an anammox-driven full-scale wastewater treatment plant.}, journal = {Water research}, volume = {235}, number = {}, pages = {119799}, doi = {10.1016/j.watres.2023.119799}, pmid = {36965294}, issn = {1879-2448}, abstract = {Microbial-driven nitrogen removal is a crucial step in modern full-scale wastewater treatment plants (WWTPs), and the complexity of nitrogen transformation is integral to the various wastewater treatment processes. A full understanding of the overall nitrogen cycling networks in WWTPs is therefore a prerequisite for the further enhancement and optimization of wastewater treatment processes. In this study, metagenomics and metatranscriptomics were used to elucidate the microbial nitrogen removal processes in an ammonium-enriched full-scale WWTP, which was configured as an anaerobic-anoxic-anaerobic-oxic system for efficient nitrogen removal (99.63%) on a duck breeding farm. A typical simultaneous nitrification-anammox-denitrification (SNAD) process was established in each tank of this WWTP. Ammonia was oxidized by ammonia-oxidizing bacteria (AOB), archaea (AOA), and nitrite-oxidizing bacteria (NOB), and the produced nitrite and nitrate were further reduced to dinitrogen gas (N2) by anammox and denitrifying bacteria. Visible red anammox biofilms were formed successfully on the sponge carriers submerged in the anoxic tank, and the nitrogen removal rate by anammox reaction was 4.85 times higher than that by denitrification based on [15]N isotope labeling and analysis. This supports the significant accumulation of anammox bacteria on the carriers responsible for efficient nitrogen removal. Two distinct anammox bacteria, named "Ca. Brocadia sp. PF01" and "Ca. Jettenia sp. PF02", were identified from the biofilm in this investigation. By recovering their genomic features and their metabolic capabilities, our results indicate that the highly active core anammox process found in PF01, suggests extending its niche within the plant. With the possible contribution of the dissimilatory nitrate reduction to ammonium (DNRA) reaction, enriching PF02 within the biofilm may also be warranted. Collectively, this study highlights the effective design strategies of a full-scale WWTP with enrichment of anammox bacteria on the carrier materials for nitrogen removal and therefore the biochemical reaction mechanisms of the contributing members.}, }
@article {pmid36965279, year = {2023}, author = {Viver, T and Conrad, RE and Lucio, M and Harir, M and Urdiain, M and Gago, JF and Suárez-Suárez, A and Bustos-Caparros, E and Sanchez-Martinez, R and Mayol, E and Fassetta, F and Pang, J and Mădălin Gridan, I and Venter, S and Santos, F and Baxter, B and Llames, ME and Cristea, A and Banciu, HL and Hedlund, BP and Stott, MB and Kämpfer, P and Amann, R and Schmitt-Kopplin, P and Konstantinidis, KT and Rossello-Mora, R}, title = {Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {3}, pages = {126416}, doi = {10.1016/j.syapm.2023.126416}, pmid = {36965279}, issn = {1618-0984}, abstract = {Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31[T], respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31[T], respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.}, }
@article {pmid36965198, year = {2023}, author = {Ceylani, T and Allahverdi, H and Teker, HT}, title = {Role of age-related plasma in the diversity of gut bacteria.}, journal = {Archives of gerontology and geriatrics}, volume = {111}, number = {}, pages = {105003}, doi = {10.1016/j.archger.2023.105003}, pmid = {36965198}, issn = {1872-6976}, abstract = {Recent studies have demonstrated the efficacy of young blood plasma factors in reversing aging-related deformities. However, the impact of plasma exchange between young and old individuals on gut microbiota remains understudied. To investigate this, we evaluated the effects of plasma exchange between 5-week-old and 24-month-old rats on gut microbiota composition. In this study, old rats were administered 0.5 ml of young plasma, while young rats were administered 0.25 ml of old plasma daily for 30 days. Metagenome analysis was performed on the contents of the cecum after completing plasma transfer. Results showed that transferring young plasma to old rats significantly increased the alpha diversity indices (Shannon and Simpson values), while the Firmicutes to Bacteroidetes ratio decreased significantly. Conversely, transferring aged plasma to young rats led to a significant decrease in Shannon value and F/B ratio but no change in Simpson value. Plasma exchange also caused substantial changes in the top ten dominant genera and species found in the gut microbiota of young and old rats. After young blood plasma transfer, the dominant bacterial profile in the old gut microbiota shifted toward the bacterial profile found in the young control group. Notably, old plasma also altered the gut microbiota structure of young rats toward that of old rats. Our findings suggest that age-related changes in plasma play a crucial role in gut microbiota species diversity and their presence rates.}, }
@article {pmid36964623, year = {2023}, author = {Manabe, Y and Ishibashi, T and Asano, R and Tonomura, S and Maeda, Y and Motooka, D and Ueda, J and Yanagawa, M and Edamoto-Taira, Y and Chikaishi-Kirino, T and Masaki, T and Inagaki, T and Nakamura, S and Katada, Y and Okazawa, M and Narazaki, M and Ogo, T and Kumanogoh, A and Nakaoka, Y}, title = {Gut dysbiosis is associated with aortic aneurysm formation and progression in Takayasu arteritis.}, journal = {Arthritis research &amp; therapy}, volume = {25}, number = {1}, pages = {46}, pmid = {36964623}, issn = {1478-6362}, abstract = {BACKGROUND: Takayasu arteritis (TAK) is an autoimmune large vessel vasculitis that affects the aorta and its major branches, eventually leading to the development of aortic aneurysm and vascular stenosis or occlusion. This retrospective and prospective study aimed to investigate whether the gut dysbiosis exists in patients with TAK and to identify specific gut microorganisms related to aortic aneurysm formation/progression in TAK.<br><br>METHODS: We analysed the faecal microbiome of 76 patients with TAK and 56 healthy controls (HCs) using 16S ribosomal RNA sequencing. We examined the relationship between the composition of the gut microbiota and clinical parameters.<br><br>RESULTS: The patients with TAK showed an altered gut microbiota with a higher abundance of oral-derived bacteria, such as Streptococcus and Campylobacter, regardless of the disease activity, than HCs. This increase was significantly associated with the administration of a proton pump inhibitor used for preventing gastric ulcers in patients treated with aspirin and glucocorticoids. Among patients taking a proton pump inhibitor, Campylobacter was more frequently detected in those who underwent vascular surgeries and endovascular therapy for aortic dilatation than in those who did not. Among the genus of Campylobacter, Campylobacter gracilis in the gut microbiome was significantly associated with clinical events related to aortic aneurysm formation/worsening in patients with TAK. In a prospective analysis, patients with a gut microbiome positive for Campylobacter were significantly more likely to require interventions for aortic dilatation than those who were negative for Campylobacter. Furthermore, patients with TAK who were positive for C. gracilis by polymerase chain reaction showed a tendency to have severe aortic aneurysms.<br><br>CONCLUSIONS: A specific increase in oral-derived Campylobacter in the gut may be a novel predictor of aortic aneurysm formation/progression in patients with TAK.}, }
@article {pmid36964199, year = {2023}, author = {Kavagutti, VS and Chiriac, MC and Ghai, R and Salcher, MM and Haber, M}, title = {Isolation of phages infecting the abundant freshwater Actinobacteriota order 'Ca. Nanopelagicales'.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36964199}, issn = {1751-7370}, abstract = {Low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of 'Ca. Nanopelagicales' we isolated a novel species of its genus 'Ca. Planktophila'. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host's metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting 'Ca. Nanopelagicales'. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.}, }
@article {pmid36964154, year = {2023}, author = {Zimmermann, HH and Stoof-Leichsenring, KR and Dinkel, V and Harms, L and Schulte, L and Hütt, MT and Nürnberg, D and Tiedemann, R and Herzschuh, U}, title = {Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1650}, pmid = {36964154}, issn = {2041-1723}, abstract = {Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.}, }
@article {pmid36963658, year = {2023}, author = {Xing, X and Liu, Q and Yuan, W and Zhu, C and Yang, J}, title = {Pulmonary scedosporiosis caused by Lomentospora prolificans in an immunocompetent patient: a rare case report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijid.2023.03.037}, pmid = {36963658}, issn = {1878-3511}, abstract = {Infections with Scedosporium and Lomentospora species are usually found in immunodeficient patients, particularly in the transplant population. However, they are relatively rare in immunocompetent patients, which is especially useful in ruling out near-drowning and aspiration situations. Here, we report a case of an immunocompetent patient with clinically suspected community-acquired pneumonia caused by Lomentospora prolificans detected by metagenomics next-generation sequencing (mNGS) and polymerase chain reaction from bronchoalveolar lavage fluid. This case highlights mNGS in the clinical diagnosis of pulmonary invasive fungal disease. mNGS is proposed as an important adjunctive diagnostic approach for rare pathogens.}, }
@article {pmid36963586, year = {2023}, author = {Dahiya, S and Mohan, SV}, title = {Co-fermenting lactic acid and glucose towards caproic acid production.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {138491}, doi = {10.1016/j.chemosphere.2023.138491}, pmid = {36963586}, issn = {1879-1298}, abstract = {The functional role of lactate (HLac), as a co-substrate along with glucose (Glu) as well as an electron donor for the synthesis of caproic acid (HCa) a medium chain fatty acids (MCFAs) was studied. A varied HLac and Glu ratios were thus investigated in fed-batch anaerobic reactors (R1-R5) operating at pH 6 with a heat-treated anaerobic consortium. R1 and R5 were noted as controls and operated with sole Glu and HLac, respectively. Strategically, ethanol (HEth) was additionally supplemented as co-electron donor after the production of short chain carboxylic acids (SCCAs) for chain elongation in all the reactors. The reactor operated with HLac and Glu in a ratio of 0.25:0.75 (1.25 g/L (HLac) and 3.75 g/L (Glu)) showed the highest HCa production of 1.86 g/L. R5 operated with solely HLac yielded propionic acid (HPr) as the major product which further led to the higher valeric acid (HVa) production of 1.1 g/L within the reactor. Butyric acid (HBu) was observed in R1, which used Glu as carbon source alone indicating the importance of HLac as electron co-donor. Clostridium observed as the most dominant genera in shotgun metagenome sequencing in R2 and R3, the reactors that produced the highest HCa in comparison to other studied reactors. The study thus provided insight into the importance of substrate and electron donor and their supplementation strategies during the production of MCFAs.}, }
@article {pmid36963164, year = {2023}, author = {Beliaeva, MA and Wilmanns, M and Zimmermann, M}, title = {Decipher enzymes from human microbiota for drug discovery and development.}, journal = {Current opinion in structural biology}, volume = {80}, number = {}, pages = {102567}, doi = {10.1016/j.sbi.2023.102567}, pmid = {36963164}, issn = {1879-033X}, abstract = {The human microbiota plays an important role in human health and contributes to the metabolism of therapeutic drugs affecting their potency. However, the current knowledge on human gut bacterial metabolism is limited and lacks an understanding of the underlying mechanisms of observed drug biotransformations. Despite the complexity of the gut microbial community, genomic and metagenomic sequencing provides insights into the diversity of chemical reactions that can be carried out by the microbiota and poses new challenges to functionally annotate thousands of bacterial enzymes. Here, we outline methods to systematically address the structural and functional space of the human microbiome, highlighting a combination of in silico and in vitro approaches. Systematic knowledge about microbial enzymes could eventually be applied for personalized therapy, the development of prodrugs and modulators of unwanted bacterial activity, and the further discovery of new antibiotics.}, }
@article {pmid36962260, year = {2022}, author = {Muthanje, EM and Kimita, G and Nyataya, J and Njue, W and Mulili, C and Mugweru, J and Mutai, B and Kituyi, SN and Waitumbi, J}, title = {March 2019 dengue fever outbreak at the Kenyan south coast involving dengue virus serotype 3, genotypes III and V.}, journal = {PLOS global public health}, volume = {2}, number = {3}, pages = {e0000122}, pmid = {36962260}, issn = {2767-3375}, abstract = {The first description of a disease resembling dengue fever (DF) was in the 15th century slave trade era by Spanish sailors visiting the Tanzania coast. The disease, then associated with evil spirits is now known to be caused by four serotypes of dengue virus (DENV1-4) that are transmitted by Aedes mosquitoes. Kenya has experienced multiple outbreaks, mostly associated with DENV-2. In this study, plasma samples obtained from 37 febrile patients during a DF outbreak at Kenya's south coast in March 2019 were screened for DENV. Total RNA was extracted and screened for the alpha- and flavi-viruses by real-time polymerase chain reaction (qPCR). DENV-3 was the only virus detected. Shotgun metagenomics and targeted sequencing were used to obtain DENV whole genomes and the complete envelope genes (E gene) respectively. Sequences were used to infer phylogenies and time-scaled genealogies. Following Maximum likelihood and Bayesian phylogenetic analysis, two DENV-3 genotypes (III, n = 15 and V, n = 2) were found. We determined that the two genotypes had been in circulation since 2015, and that both had been introduced independently. Genotype III's origin was estimated to have been from Pakistan. Although the origin of genotype V could not be ascertained due to rarity of these sequences globally, it was most related to a 2006 Brazilian isolate. Unlike genotype III that has been described in East and West Africa multiple times, this was the second description of genotype V in Kenya. Of note, there was marked amino acid variances in the E gene between study samples and the Thailand DENV-3 strain used in the approved Dengvaxia vaccine. It remains to be seen whether these variances negatively impact the efficacy of the Dengvaxia or future vaccines.}, }
@article {pmid36961862, year = {2023}, author = {Yan, W and Zhu, Y and Liu, W and Zou, C and Jia, B and Chen, ZQ and Han, Y and Wu, J and Yang, DL and Zhang, Z and Xie, L and Chen, B and Li, R and Ding, SW and Wu, Q and Guo, Z}, title = {Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing.}, journal = {PLoS pathogens}, volume = {19}, number = {3}, pages = {e1011238}, doi = {10.1371/journal.ppat.1011238}, pmid = {36961862}, issn = {1553-7374}, abstract = {A major threat to rice production is the disease epidemics caused by insect-borne viruses that emerge and re-emerge with undefined origins. It is well known that some human viruses have zoonotic origins from wild animals. However, it remains unknown whether native plants host uncharacterized endemic viruses with spillover potential to rice (Oryza sativa) as emerging pathogens. Here, we discovered rice tiller inhibition virus (RTIV), a novel RNA virus species, from colonies of Asian wild rice (O. rufipogon) in a genetic reserve by metagenomic sequencing. We identified the specific aphid vector that is able to transmit RTIV and found that RTIV would cause low-tillering disease in rice cultivar after transmission. We further demonstrated that an infectious molecular clone of RTIV initiated systemic infection and causes low-tillering disease in an elite rice variety after Agrobacterium-mediated inoculation or stable plant transformation, and RTIV can also be transmitted from transgenic rice plant through its aphid vector to cause disease. Finally, global transcriptome analysis indicated that RTIV may disturb defense and tillering pathway to cause low tillering disease in rice cultivar. Thus, our results show that new rice viral pathogens can emerge from native habitats, and RTIV, a rare aphid-transmitted rice viral pathogen from native wild rice, can threaten the production of rice cultivar after spillover.}, }
@article {pmid36961286, year = {2023}, author = {López-Islas, JJ and Méndez-Olvera, ET and Reyes C, T and Martínez-Gómez, D}, title = {Identification of antimicrobial resistance genes in intestinal content from Coyote (Canis latrans).}, journal = {Polish journal of veterinary sciences}, volume = {26}, number = {1}, pages = {143-149}, doi = {10.24425/pjvs.2023.145016}, pmid = {36961286}, issn = {2300-2557}, abstract = {Antibiotic resistance has become a global public health concern in the last few years. Given the widespread rate of recurrence, increasing attention is being turned toward environmental pathways that potentially contribute to antibiotic resistance genes (ARGs) dissemination outside the clinical realm. In this study, a metagenome analysis of intestinal virus-like particle fraction (VLPs) from a wild coyote (Canis latrans) revealed for the first time, multiple ARGs, such as B-lactamases and multidrug efflux pumps. Description of ARGs presence in natural environments is critical to understand the emergence of resistant strains.}, }
@article {pmid36960290, year = {2023}, author = {Marini, S and Boucher, C and Noyes, N and Prosperi, M}, title = {The K-mer antibiotic resistance gene variant analyzer (KARGVA).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1060891}, pmid = {36960290}, issn = {1664-302X}, abstract = {Characterization of antibiotic resistance genes (ARGs) from high-throughput sequencing data of metagenomics and cultured bacterial samples is a challenging task, with the need to account for both computational (e.g., string algorithms) and biological (e.g., gene transfers, rearrangements) aspects. Curated ARG databases exist together with assorted ARG classification approaches (e.g., database alignment, machine learning). Besides ARGs that naturally occur in bacterial strains or are acquired through mobile elements, there are chromosomal genes that can render a bacterium resistant to antibiotics through point mutations, i.e., ARG variants (ARGVs). While ARG repositories also collect ARGVs, there are only a few tools that are able to identify ARGVs from metagenomics and high throughput sequencing data, with a number of limitations (e.g., pre-assembly, a posteriori verification of mutations, or specification of species). In this work we present the k-mer, i.e., strings of fixed length k, ARGV analyzer - KARGVA - an open-source, multi-platform tool that provides: (i) an ad hoc, large ARGV database derived from multiple sources; (ii) input capability for various types of high-throughput sequencing data; (iii) a three-way, hash-based, k-mer search setup to process data efficiently, linking k-mers to ARGVs, k-mers to point mutations, and ARGVs to k-mers, respectively; (iv) a statistical filter on sequence classification to reduce type I and II errors. On semi-synthetic data, KARGVA provides very high accuracy even in presence of high sequencing errors or mutations (99.2 and 86.6% accuracy within 1 and 5% base change rates, respectively), and genome rearrangements (98.2% accuracy), with robust performance on ad hoc false positive sets. On data from the worldwide MetaSUB consortium, comprising 3,700+ metagenomics experiments, KARGVA identifies more ARGVs than Resistance Gene Identifier (4.8x) and PointFinder (6.8x), yet all predictions are below the expected false positive estimates. The prevalence of ARGVs is correlated to ARGs but ecological characteristics do not explain well ARGV variance. KARGVA is publicly available at https://github.com/DataIntellSystLab/KARGVA under MIT license.}, }
@article {pmid36960043, year = {2023}, author = {Lin, T}, title = {Editorial: New techniques in microbiome research.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1158392}, doi = {10.3389/fcimb.2023.1158392}, pmid = {36960043}, issn = {2235-2988}, }
@article {pmid36959975, year = {2023}, author = {Baltoumas, FA and Karatzas, E and Paez-Espino, D and Venetsianou, NK and Aplakidou, E and Oulas, A and Finn, RD and Ovchinnikov, S and Pafilis, E and Kyrpides, NC and Pavlopoulos, GA}, title = {Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1157956}, pmid = {36959975}, issn = {2673-7647}, abstract = {Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.}, }
@article {pmid36959686, year = {2023}, author = {Yang, Y and Han, Z and Gao, Z and Chen, J and Song, C and Xu, J and Wang, H and Huang, A and Shi, J and Gu, J}, title = {Metagenomic and targeted metabolomic analyses reveal distinct phenotypes of the gut microbiota in patients with colorectal cancer and type 2 diabetes mellitus.}, journal = {Chinese medical journal}, volume = {}, number = {}, pages = {}, pmid = {36959686}, issn = {2542-5641}, abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is an independent risk factor for colorectal cancer (CRC), and the patients with CRC and T2DM have worse survival. The human gut microbiota (GM) is linked to the development of CRC and T2DM, respectively. However, the GM characteristics in patients with CRC and T2DM remain unclear.<br><br>METHODS: We performed fecal metagenomic and targeted metabolomics studies on 36 samples from CRC patients with T2DM (DCRC group, n = 12), CRC patients without diabetes (CRC group, n = 12), and healthy controls (Health group, n = 12). We analyzed the fecal microbiomes, characterized the composition and function based on the metagenomics of DCRC patients, and detected the short-chain fatty acids (SCFAs) and bile acids (BAs) levels in all fecal samples. Finally, we performed a correlation analysis of the differential bacteria and metabolites between different groups.<br><br>RESULTS: Compared with the CRC group, LefSe analysis showed that there is a specific GM community in DCRC group, including an increased abundance of Eggerthella, Hungatella, Peptostreptococcus, and Parvimonas, and decreased Butyricicoccus, Lactobacillus, and Paraprevotella. The metabolomics analysis results revealed that the butyric acid level was lower but the deoxycholic acid and 12-keto-lithocholic acid levels were higher in the DCRC group than other groups (P < 0.05). The correlation analysis showed that the dominant bacterial abundance in the DCRC group (Parvimonas, Desulfurispora, Sebaldella, and Veillonellales, among others) was negatively correlated with butyric acid, hyodeoxycholic acid, ursodeoxycholic acid, glycochenodeoxycholic acid, chenodeoxycholic acid, cholic acid and glycocholate. However, the abundance of mostly inferior bacteria was positively correlated with these metabolic acid levels, including Faecalibacterium, Thermococci, and Cellulophaga.<br><br>CONCLUSIONS: Unique fecal microbiome signatures exist in CRC patients with T2DM compared to those with non-diabetic CRC. Alterations in GM composition and SCFAs and secondary BAs levels may promote CRC development.}, }
@article {pmid36959175, year = {2023}, author = {Bjerg, JJ and Lustermans, JJM and Marshall, IPG and Mueller, AJ and Brokjær, S and Thorup, CA and Tataru, P and Schmid, M and Wagner, M and Nielsen, LP and Schramm, A}, title = {Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1614}, pmid = {36959175}, issn = {2041-1723}, abstract = {Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.}, }
@article {pmid36958817, year = {2023}, author = {Vich Vila, A and Hu, S and Andreu-Sánchez, S and Collij, V and Jansen, BH and Augustijn, HE and Bolte, LA and Ruigrok, RAAA and Abu-Ali, G and Giallourakis, C and Schneider, J and Parkinson, J and Al-Garawi, A and Zhernakova, A and Gacesa, R and Fu, J and Weersma, RK}, title = {Faecal metabolome and its determinants in inflammatory bowel disease.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2022-328048}, pmid = {36958817}, issn = {1468-3288}, abstract = {OBJECTIVE: Inflammatory bowel disease (IBD) is a multifactorial immune-mediated inflammatory disease of the intestine, comprising Crohn's disease and ulcerative colitis. By characterising metabolites in faeces, combined with faecal metagenomics, host genetics and clinical characteristics, we aimed to unravel metabolic alterations in IBD.<br><br>DESIGN: We measured 1684 different faecal metabolites and 8 short-chain and branched-chain fatty acids in stool samples of 424 patients with IBD and 255 non-IBD controls. Regression analyses were used to compare concentrations of metabolites between cases and controls and determine the relationship between metabolites and each participant's lifestyle, clinical characteristics and gut microbiota composition. Moreover, genome-wide association analysis was conducted on faecal metabolite levels.<br><br>RESULTS: We identified over 300 molecules that were differentially abundant in the faeces of patients with IBD. The ratio between a sphingolipid and L-urobilin could discriminate between IBD and non-IBD samples (AUC=0.85). We found changes in the bile acid pool in patients with dysbiotic microbial communities and a strong association between faecal metabolome and gut microbiota. For example, the abundance of Ruminococcus gnavus was positively associated with tryptamine levels. In addition, we found 158 associations between metabolites and dietary patterns, and polymorphisms near NAT2 strongly associated with coffee metabolism.<br><br>CONCLUSION: In this large-scale analysis, we identified alterations in the metabolome of patients with IBD that are independent of commonly overlooked confounders such as diet and surgical history. Considering the influence of the microbiome on faecal metabolites, our results pave the way for future interventions targeting intestinal inflammation.}, }
@article {pmid36958333, year = {2023}, author = {Begg, TJA and Schmidt, A and Kocher, A and Larmuseau, MHD and Runfeldt, G and Maier, PA and Wilson, JD and Barquera, R and Maj, C and Szolek, A and Sager, M and Clayton, S and Peltzer, A and Hui, R and Ronge, J and Reiter, E and Freund, C and Burri, M and Aron, F and Tiliakou, A and Osborn, J and Behar, DM and Boecker, M and Brandt, G and Cleynen, I and Strassburg, C and Prüfer, K and Kühnert, D and Meredith, WR and Nöthen, MM and Attenborough, RD and Kivisild, T and Krause, J}, title = {Genomic analyses of hair from Ludwig van Beethoven.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2023.02.041}, pmid = {36958333}, issn = {1879-0445}, abstract = {Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry.}, }
@article {pmid36958260, year = {2023}, author = {Sugiyama, Y and Takata, K and Kinoshita, M and Motooka, D and Shiraishi, N and Kihara, K and Murata, H and Beppu, S and Koda, T and Yamashita, K and Namba, A and Fujimoto, K and Kumanogoh, A and Okuno, T and Mochizuki, H}, title = {Food additive succinate exacerbates experimental autoimmune encephalomyelitis accompanied by increased IL-1β production.}, journal = {Biochemical and biophysical research communications}, volume = {656}, number = {}, pages = {97-103}, doi = {10.1016/j.bbrc.2023.03.041}, pmid = {36958260}, issn = {1090-2104}, }
@article {pmid36958034, year = {2023}, author = {Farrington, M and Elenz, J and Ginsberg, M and Chiu, CY and Miller, S and Pangonis, SF}, title = {Powassan Virus Infection Detected by Metagenomic Next-Generation Sequencing, Ohio, USA.}, journal = {Emerging infectious diseases}, volume = {29}, number = {4}, pages = {838-841}, doi = {10.3201/eid2904.221005}, pmid = {36958034}, issn = {1080-6059}, abstract = {We describe a 4-year-old male patient in Ohio, USA, who had encephalitis caused by Powassan virus lineage 2. Virus was detected by using metagenomic next-generation sequencing and confirmed with IgM and plaque reduction neutralization assays. Clinicians should recognize changing epidemiology of tickborne viruses to enhance encephalitis diagnosis and management.}, }
@article {pmid36957994, year = {2023}, author = {Martin, NA and Gonzalez, G and Reynolds, LJ and Bennett, C and Campbell, C and Nolan, TM and Byrne, A and Fennema, S and Holohan, N and Kuntamukkula, SR and Sarwar, N and Sala-Comorera, L and Dean, J and Urtasun-Elizari, JM and Hare, D and Liddy, E and Joyce, E and O'Sullivan, JJ and Cuddihy, JM and McIntyre, AM and Robinson, EP and Dahly, D and Fletcher, NF and Cotter, S and Fitzpatrick, E and Carr, MJ and De Gascun, CF and Meijer, WG}, title = {Adeno-Associated Virus 2 and Human Adenovirus F41 in Wastewater during Outbreak of Severe Acute Hepatitis in Children, Ireland.}, journal = {Emerging infectious diseases}, volume = {29}, number = {4}, pages = {751-760}, doi = {10.3201/eid2904.221878}, pmid = {36957994}, issn = {1080-6059}, abstract = {During April-July 2022, outbreaks of severe acute hepatitis of unknown etiology (SAHUE) were reported in 35 countries. Five percent of cases required liver transplantation, and 22 patients died. Viral metagenomic studies of clinical samples from SAHUE cases showed a correlation with human adenovirus F type 41 (HAdV-F41) and adeno-associated virus type 2 (AAV2). To explore the association between those DNA viruses and SAHUE in children in Ireland, we quantified HAdV-F41 and AAV2 in samples collected from a wastewater treatment plant serving 40% of Ireland's population. We noted a high correlation between HAdV-F41 and AAV2 circulation in the community and SAHUE clinical cases. Next-generation sequencing of the adenovirus hexon in wastewater demonstrated HAdV-F41 was the predominant HAdV type circulating. Our environmental analysis showed increased HAdV-F41 and AAV2 prevalence in the community during the SAHUE outbreak. Our findings highlight how wastewater sampling could aid in surveillance for respiratory adenovirus species.}, }
@article {pmid36952228, year = {2023}, author = {Lai, JL and Li, ZG and Wang, Y and Xi, HL and Luo, XG}, title = {Tritium and Carbon-14 Contamination Reshaping the Microbial Community Structure, Metabolic Network, and Element Cycle in the Seawater Environment.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c00422}, pmid = {36952228}, issn = {1520-5851}, abstract = {The potential ecological risks caused by entering radioactive wastewater containing tritium and carbon-14 into the sea require careful evaluation. This study simulated seawater's tritium and carbon-14 pollution and analyzed the effects on the seawater and sediment microenvironments. Tritium and carbon-14 pollution primarily altered nitrogen and phosphorus metabolism in the seawater environment. Analysis by 16S rRNA sequencing showed changes in the relative abundance of microorganisms involved in carbon, nitrogen, and phosphorus metabolism and organic matter degradation in response to tritium and carbon-14 exposure. Metabonomics and metagenomic analysis showed that tritium and carbon-14 exposure interfered with gene expression involving nucleotide and amino acid metabolites, in agreement with the results seen for microbial community structure. Tritium and carbon-14 exposure also modulated the abundance of functional genes involved in carbohydrate, phosphorus, sulfur, and nitrogen metabolic pathways in sediments. Tritium and carbon-14 pollution in seawater adversely affected microbial diversity, metabolic processes, and the abundance of nutrient-cycling genes. These results provide valuable information for further evaluating the risks of tritium and carbon-14 in marine environments.}, }
@article {pmid36951567, year = {2023}, author = {Goswami, A and Adkins-Jablonsky, SJ and Barreto Filho, MM and Shilling, MD and Dawson, A and Heiser, S and O'Connor, A and Walker, M and Roberts, Q and Morris, JJ}, title = {Heavy Metal Pollution Impacts Soil Bacterial Community Structure and Antimicrobial Resistance at the Birmingham 35th Avenue Superfund Site.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0242622}, doi = {10.1128/spectrum.02426-22}, pmid = {36951567}, issn = {2165-0497}, abstract = {Heavy metals (HMs) are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease. IMPORTANCE Heavy metals cross-select for antimicrobial resistance in laboratory experiments, but few studies have documented this effect in polluted soils. Moreover, despite decades of awareness of heavy metal contamination at the EPA Superfund site in North Birmingham, Alabama, this is the first analysis of the impact of this pollution on the soil microbiome. Specifically, this work advances the understanding of the relationship between heavy metals, microbial diversity, and patterns of antibiotic resistance in North Birmingham soils. Our results suggest that polluted soils carry a risk of increased exposure to antibiotic-resistant infections in addition to the direct health consequences of heavy metals. Our work provides important information relevant to both political and scientific efforts to advance environmental justice for the communities that call Superfund neighborhoods home.}, }
@article {pmid36951557, year = {2023}, author = {Wells, M and Kim, M and Akob, DM and Basu, P and Stolz, JF}, title = {Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0414522}, doi = {10.1128/spectrum.04145-22}, pmid = {36951557}, issn = {2165-0497}, abstract = {The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO2 reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere. IMPORTANCE The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have coevolved over deep time to how anaerobic life adapted to increasing concentrations of O2 during the transition from an anoxic to an oxic world. Our work emphasizes that phylogenetic analyses can reveal how domain gain or loss events, the acquisition of novel partner subunits, and the loss of metal cofactors can stimulate novel radiations of enzymes that dramatically increase the catalytic versatility of superfamilies. We also contend that the superfamily concept in protein evolution can uncover surprising kinships between enzymes that have remarkably different catalytic and physiological functions.}, }
@article {pmid36951555, year = {2023}, author = {Chu, Y and Meng, Q and Yu, J and Zhang, J and Chen, J and Kang, Y}, title = {Strain-Level Dynamics Reveal Regulatory Roles in Atopic Eczema by Gut Bacterial Phages.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0455122}, doi = {10.1128/spectrum.04551-22}, pmid = {36951555}, issn = {2165-0497}, abstract = {The vast population of bacterial phages or viruses (virome) plays pivotal roles in the ecology of human microbial flora and health conditions. Obstacles, including poor viral sequence inference, strain-sensitive virus-host relationship, and the high diversity among individuals, hinder the in-depth understanding of the human virome. We conducted longitudinal studies of the virome based on constructing a high-quality personal reference metagenome (PRM). By applying long-read sequencing for representative samples, we could build a PRM of high continuity that allows accurate annotation and abundance estimation of viruses and bacterial species in all samples of the same individual by aligning short sequencing reads to the PRM. We applied this approach to a series of fecal samples collected for 6 months from a 2-year-old boy who had experienced a 2-month flare-up of atopic eczema (dermatitis) in this period. We identified 31 viral strains in the patient's gut microbiota and deciphered their strain-level relationship to their bacterial hosts. Among them, a lytic crAssphage developed into a dozen substrains and coordinated downregulation in the catabolism of aromatic amino acids (AAAs) in their host bacteria which govern the production of immune-active AAA derivates. The metabolic alterations confirmed based on metabolomic assays cooccurred with symptom remission. Our PRM-based analysis provides an easy approach for deciphering the dynamics of the strain-level human gut virome in the context of entire microbiota. Close temporal correlations among virome alteration, microbial metabolism, and disease remission suggest a potential mechanism for how bacterial phages in microbiota are intimately related to human health. IMPORTANCE The vast populations of viruses or bacteriophages in human gut flora remain mysterious. However, poor annotation and abundance estimation remain obstacles to strain-level analysis and clarification of their roles in microbiome ecology and metabolism associated with human health and diseases. We demonstrate that a personal reference metagenome (PRM)-based approach provides strain-level resolution for analyzing the gut microbiota-associated virome. When applying such an approach to longitudinal samples collected from a 2-year-old boy who has experienced a 2-month flare-up of atopic eczema, we observed thriving substrains of a lytic crAssphage, showing temporal correlation with downregulated catabolism of aromatic amino acids, lower production of immune-active metabolites, and remission of the disease. The PRM-based approach is practical and powerful for strain-centric analysis of the human gut virome, and the underlying mechanism of how strain-level virome dynamics affect disease deserves further investigation.}, }
@article {pmid36950986, year = {2023}, author = {Gao, B and Shi, X and Li, S and Xu, W and Gao, N and Shan, J and Shen, W}, title = {Size-dependent effects of polystyrene microplastics on gut metagenome and antibiotic resistance in C57BL/6 mice.}, journal = {Ecotoxicology and environmental safety}, volume = {254}, number = {}, pages = {114737}, doi = {10.1016/j.ecoenv.2023.114737}, pmid = {36950986}, issn = {1090-2414}, abstract = {Microplastic pollution is an emerging threat for marine and terrestrial ecosystems, which has raised global concerns about its implications for human health. Mounting evidence has shown that the gut microbiota plays a key role in human health and diseases. The gut bacteria could be disturbed by many environmental factors, including the microplastic particles. However, the size effect of polystyrene microplastics on mycobiome, as well as gut functional metagenome has not been well studied. In this study, we performed ITS sequencing to explore the size effect of polystyrene microplastics on the fungal composition, in combination with the shotgun metagenomics sequencing to reveal the size effects of polystyrene on the functional metagenome. We found that polystyrene microplastic particles with 0.05-0.1 µm diameter showed greater impact on the bacterial and fungal composition of gut microbiota as well as the metabolic pathways than the polystyrene microplastic particles with 9-10 µm diameter. Our results suggested that size-depended effects should not be ignored in the health risk assessment of microplastics.}, }
@article {pmid36950589, year = {2023}, author = {Fabunmi, BT and Adegaye, AC and Ogunjo, ST}, title = {Identification and characterization of molecular entities differentially expressed in bacteria genome upon treatment with glyphosate shock.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e13868}, pmid = {36950589}, issn = {2405-8440}, abstract = {Antimetabolites developed from enzymes in the shikimate pathway are appealing targets. There are, however, certain unidentified molecular entities that show bacterial sensitivity to glyphosate shock. This study aims to identify the expression pattern of such entities following treatment with glyphosate shock and to characterize them structurally and functionally. Understanding such entities' catalytic structure and modulatory role guides the design and development of novel antibiotics. This study's functional profiling of 16S rRNA sequencing data and transcriptome analysis of glyphosate-exposedE. coli revealed that two genes were upregulated and twenty-eight were downregulated after glyphosate shock. We discovered the differential expression of some processes based on functional gene analysis, such as global and overview maps (4.2195 on average), carbohydrate metabolism (0.6858 on average), amino acid metabolism (0.5032 on average), and co-factor and vitamin metabolism (0.5032 on average) (0.2876 on average). After examining the two data sets, we discovered that some unidentified proteins were strongly expressed after glyphosate treatment. After examining the two datasets, we discovered a protein with no unique features expressed when treated with glyphosate. The Ecs2020 model looks to be the most stable in structural modeling investigations, while the catalytic residues sought in drug development are anticipated. Furthermore, biological processes and cellular component enrichment analysis revealed that the differentially expressed genes were strongly related to the trehalose manufacturing process and represented the cell membrane's outer membrane component. To estimate the functional gene content of soil sample metagenomics based on 16S rRNA, predictive functional analysis was done with R using the Tax4Fun2 package. On the other hand, transcriptome analysis was carried out using the R tool GEO2R. The results could be a good starting point for making new antibiotic medicines.}, }
@article {pmid36950329, year = {2023}, author = {Han, J and Kong, T and Jiang, J and Zhao, X and Zhao, X and Li, P and Gu, Q}, title = {Characteristic flavor metabolic network of fish sauce microbiota with different fermentation processes based on metagenomics.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1121310}, pmid = {36950329}, issn = {2296-861X}, abstract = {This article purposed to discuss the connection between microbiota and characteristic flavor of different fish sauces (Natural fermentation (WQ), koji outdoor fermentation (YQ), heat preservation with enzyme (BWE), and heat preservation with koji (BWQ)) at the early (3 months) and late stage (7 months). A total of 117 flavor compounds were determined according to SPME-GC-MS analysis. O2PLS-DA and VIP values were used to reveal 15 and 28 flavor markers of different fish sauces at 3 and 7 M of fermentation. Further, the possible flavor formation pathways were analyzed using metagenomic sequencing, and the key microbes associated with flavor formation were identified at the genetic level. The top 10 genera related to flavor generation, such as Lactobacillus, Staphylococcus, Enterobacter, etc., appeared to play a prominent part in the flavor formation of fish sauce. The difference was that only BWQ and BWE groups could produce ethyl-alcohol through amino acid metabolism, while YQ, BWE and BWQ groups could generate phenylacetaldehyde through the transformation of Phe by α-ketoacid decarboxylase and aromatic amino acid transferase. Our research contributes to clarifying the various metabolic roles of microorganisms in the flavor generation of fish sauce.}, }
@article {pmid36950183, year = {2023}, author = {Luciola Zanette, D and Andrade Coelho, KBC and de Carvalho, E and Aoki, MN and Nardin, JM and Araújo Lalli, L and Dos Santos Bezerra, R and Giovanetti, M and Simionatto Zucherato, V and Montenegro de Campos, G and de Souza Todão Bernardino, J and Louis Viala, V and Ciccozzi, M and Junior Alcantara, LC and Coccuzzo Sampaio, S and Elias, MC and Kashima, S and Tadeu Covas, D and Nanev Slavov, S}, title = {Metagenomic insights into the plasma virome of Brazilian patients with prostate cancer.}, journal = {Molecular &amp; cellular oncology}, volume = {10}, number = {1}, pages = {2188858}, pmid = {36950183}, issn = {2372-3556}, abstract = {Growing evidence suggests that metavirome changes could be associated increased risk for malignant cell transformation. Considering Viruses have been proposed as factors for prostate cancer induction. The objective of this study was to examine the composition of the plasma metavirome of patients with prostate cancer. Blood samples were obtained from 49 male patients with primary prostate adenocarcinoma. Thirty blood donors were included as a control group. The obtained next-generation sequencing data were analyzed using a bioinformatic pipeline for virus metagenomics. Viral reads with higher abundance were assembled in contigs and analyzed taxonomically. Viral agents of interest were also confirmed by qPCR. Anelloviruses and the Human Pegivirus-1 (HPgV-1) were the most abundant component of plasma metavirome. Clinically important viruses like hepatitis C virus (HCV), cytomegalovirus and human adenovirus type C were also identified. In comparison, the blood donor virome was exclusively composed of torque teno virus types (TTV) types. The performed HPgV-1 and HCV phylogeny revealed that these viruses belong to commonly detected in Brazil genotypes. Our study sheds light on the plasma viral abundance in patients with prostatic cancer. The obtained viral diversity allowed us to separate the patients and controls, probably suggesting that malignant processes may influence virome composition. More complex and multiple approach investigations are necessary to examine the likely causal relationship between metavirome and its nvolvement in prostate cancer.}, }
@article {pmid36949817, year = {2023}, author = {Viehweger, A and Marquet, M and Hölzer, M and Dietze, N and Pletz, MW and Brandt, C}, title = {Nanopore-based enrichment of antimicrobial resistance genes - a case-based study.}, journal = {GigaByte (Hong Kong, China)}, volume = {2023}, number = {}, pages = {gigabyte75}, pmid = {36949817}, issn = {2709-4715}, abstract = {Rapid screening of hospital admissions to detect asymptomatic carriers of resistant bacteria can prevent pathogen outbreaks. However, the resulting isolates rarely have their genome sequenced due to cost constraints and long turn-around times to get and process the data, limiting their usefulness to the practitioner. Here we used real-time, on-device target enrichment ("adaptive") sequencing as a highly multiplexed assay covering 1,147 antimicrobial resistance genes. We compared its utility against standard and metagenomic sequencing, focusing on an isolate of Raoultella ornithinolytica harbouring three carbapenemases (NDM, KPC, VIM). Based on this experimental data, we then modelled the influence of several variables on the enrichment results and predicted the large effect of nucleotide identity (higher is better) and read length (shorter is better). Lastly, we showed how all relevant resistance genes are detected using adaptive sequencing on a miniature ("Flongle") flow cell, motivating its use in a clinical setting to monitor similar cases and their surroundings.}, }
@article {pmid36949609, year = {2023}, author = {Hagh-Doust, N and Mikryukov, V and Anslan, S and Bahram, M and Puusepp, R and Dulya, O and Tedersoo, L}, title = {Effects of nitrogen deposition on carbon and nutrient cycling along a natural soil acidity gradient as revealed by metagenomics.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18897}, pmid = {36949609}, issn = {1469-8137}, abstract = {Nitrogen (N) deposition and soil acidification are environmental challenges affecting ecosystem functioning, health, and biodiversity, but their effects on functional genes are poorly understood. Here, we utilized metabarcoding and metagenomics to investigate the responses of soil functional genes to N deposition along a natural soil pH gradient. Soil N content was uncorrelated with pH, enabling us to investigate their effects separately. Soil acidity strongly and negatively affected the relative abundances of most cluster of orthologous gene (COG) categories of the metabolism supercategory. Similarly, soil acidity negatively affected the diversity of functional genes related to carbon and N but not phosphorus cycling. Multivariate analyses showed that soil pH was the most important factor affecting microbial and functional gene composition, while the effects of N deposition were less important. Relative abundance of KEGG functional modules related to different parts of the studied cycles showed variable responses to soil acidity and N deposition. Furthermore, our results suggested that the diversity-function relationship reported for other organisms also applies to soil microbiomes. Since N deposition and soil pH affected microbial taxonomic and functional composition to a different extent, we conclude that N deposition effects might be primarily mediated through soil acidification in forest ecosystems.}, }
@article {pmid36949545, year = {2023}, author = {Graham, EH and Tom, WA and Neujahr, AC and Adamowicz, MS and Clarke, JL and Herr, JR and Fernando, SC}, title = {The persistence and stabilization of auxiliary genes in the human skin virome.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {49}, pmid = {36949545}, issn = {1743-422X}, abstract = {BACKGROUND: The human skin contains a diverse microbiome that provides protective functions against environmental pathogens. Studies have demonstrated that bacteriophages modulate bacterial community composition and facilitate the transfer of host-specific genes, potentially influencing host cellular functions. However, little is known about the human skin virome and its role in human health. Especially, how viral-host relationships influence skin microbiome structure and function is poorly understood.<br><br>RESULTS: Population dynamics and genetic diversity of bacteriophage communities in viral metagenomic data collected from three anatomical skin locations from 60 subjects at five different time points revealed that cutaneous bacteriophage populations are mainly composed of tailed Caudovirales phages that carry auxiliary genes to help improve metabolic remodeling to increase bacterial host fitness through antimicrobial resistance. Sequence variation in the MRSA associated antimicrobial resistance gene, erm(C) was evaluated using targeted sequencing to further confirm the presence of antimicrobial resistance genes in the human virome and to demonstrate how functionality of such genes may influence persistence and in turn stabilization of bacterial host and their functions.<br><br>CONCLUSIONS: This large temporal study of human skin associated viruses indicates that the human skin virome is associated with auxiliary metabolic genes and antimicrobial resistance genes to help increase bacterial host fitness.}, }
@article {pmid36949471, year = {2023}, author = {Volmer, JG and Soo, RM and Evans, PN and Hoedt, EC and Astorga Alsina, AL and Woodcroft, BJ and Tyson, GW and Hugenholtz, P and Morrison, M}, title = {Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {59}, pmid = {36949471}, issn = {1741-7007}, abstract = {BACKGROUND: With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with 'low-methane' emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum, as well as Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales. Despite sporadic reports of Methanocorpusculum from stool samples of various animal species, there remains little information on the impacts of these methanogens on their hosts.<br><br>RESULTS: Here, we characterise novel host-associated species of Methanocorpusculum, to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat (Vombatus ursinus) and mahogany glider (Petaurus gracilis), along with the cultivation of one axenic isolate from each respective animal; M. vombati (sp. nov.) and M. petauri (sp. nov.).<br><br>CONCLUSIONS: Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum. These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated.}, }
@article {pmid36949342, year = {2023}, author = {Nosalova, L and Kiskova, J and Fecskeova, LK and Piknova, M and Pristas, P}, title = {Bacterial Community Structure of Two Cold Sulfur Springs in Slovakia (Central Europe).}, journal = {Current microbiology}, volume = {80}, number = {5}, pages = {145}, pmid = {36949342}, issn = {1432-0991}, abstract = {Sulfur-oxidizing bacteria, especially those from hot springs, have attracted the attention of microbiologists for more than 150 years. In contrast, the microbial diversity of cold sulfur springs remains largely unrecognized. Culture-dependent and culture-independent approaches were used to study the diversity of sulfur-oxidizing bacterial communities in two cold sulfur springs in Slovakia. Geological conditions and resulting spring water chemistry appear to be major factors influencing the composition of the sulfur-oxidizing bacterial community. Bacterial communities in both springs were found to be dominated by Proteobacteria with Epsilonproteobacteria being prevalent in the high-salinity Stankovany spring and Alpha- and Gammaproteobacteria in the low-salinity Jovsa spring. Limited overlap was found between culture-dependent and culture-independent approaches with multiple taxa of cultivated sulfur-oxidizing bacteria not being detected by the culture-independent metagenomics approach. Moreover, four cultivated bacterial isolates could represent novel taxa based on the low similarity of their 16S rRNA gene sequence (similarity lower than 98%) to sequences of known bacteria. Our study supports the current view that multiple approaches are required to assess the bacterial diversity in natural habitats and indicates that sulfur springs in Slovakia harbor unique, yet-undescribed microorganisms.}, }
@article {pmid36949220, year = {2023}, author = {Lynes, MM and Krukenberg, V and Jay, ZJ and Kohtz, AJ and Gobrogge, CA and Spietz, RL and Hatzenpichler, R}, title = {Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {22}, pmid = {36949220}, issn = {2730-6151}, abstract = {Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.}, }
@article {pmid36948449, year = {2023}, author = {Wang, C and Wang, J and Yan, J and Chen, F and Zhang, Y and Hu, X}, title = {Mycoplasma hominis, Ureaplasma parvum and Ureaplasma urealyticum: hidden pathogens in peritoneal dialysis-associated peritonitis.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijid.2023.03.032}, pmid = {36948449}, issn = {1878-3511}, abstract = {BACKGROUND: Mycoplasma hominis, Ureaplasma parvum, and Ureaplasma urealyticum commonly colonize the human urogenital tract which may cause urogenital infections. However, infection by M. hominis, U. parvum, or U. urealyticum is rarely reported in peritoneal dialysis (PD) associated peritonitis patients. Herein, we reported four cases of PD-associated peritonitis caused by these pathogens, along with a review of the literature.<br><br>CASE REPORT: The four cases were female patients with recurrent "culture-negative" PD-associated peritonitis and were related to menstruation. M. hominis, U. parvum, or U. urealyticum was detected in the peritoneal dialysis fluid of the patients by metagenomic next-generation sequencing (mNGS). All four patients were cured by intraperitoneal (IP) tigecycline combined with oral azithromycin or minocycline.<br><br>CONCLUSIONS: M. hominis, U. parvum, and U. urealyticum should be paid more attention in female patients suffering from recurrent "culture-negative" PD-associated peritonitis, especially when the peritonitis is related to menstruation, sexual intercourse, or urogenital tract operation. Moreover, mNGS can provide a reasonable method to identify the pathogen for "culture-negative" PD-associated peritonitis.}, }
@article {pmid36948151, year = {2023}, author = {Toh, E and Xing, Y and Gao, X and Jordan, SJ and Batteiger, TA and Batteiger, BE and Van Der Pol, B and Muzny, CA and Gebregziabher, N and Williams, JA and Fortenberry, LJ and Fortenberry, JD and Dong, Q and Nelson, DE}, title = {Sexual behavior shapes male genitourinary microbiome composition.}, journal = {Cell reports. Medicine}, volume = {4}, number = {3}, pages = {100981}, doi = {10.1016/j.xcrm.2023.100981}, pmid = {36948151}, issn = {2666-3791}, abstract = {The origin, composition, and significance of the distal male urethral microbiome are unclear, but vaginal microbiome dysbiosis is linked to new sex partners and several urogynecological syndromes. We characterized 110 urethral specimens from men without urethral symptoms, infections, or inflammation using shotgun metagenomics. Most urethral specimens contain characteristic lactic acid bacteria and Corynebacterium spp. In contrast, several bacteria associated with vaginal dysbiosis were present only in specimens from men who reported vaginal intercourse. Sexual behavior, but not other evaluated behavioral, demographic, or clinical variables, strongly associated with inter-specimen variance in urethral microbiome composition. Thus, the male urethra supports a simple core microbiome that is established independent of sexual exposures but can be re-shaped by vaginal sex. Overall, the results suggest that urogenital microbiology and sexual behavior are inexorably intertwined, and show that the male urethra harbors female urogenital pathobionts.}, }
@article {pmid36947490, year = {2023}, author = {Highlander, SK and Wood, JM and Gillece, JD and Folkerts, M and Fofanov, V and Furstenau, T and Singh, NK and Guan, L and Seuylemezian, A and Benardini, JN and Engelthaler, DM and Venkateswaran, K and Keim, PS}, title = {Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0282428}, doi = {10.1371/journal.pone.0282428}, pmid = {36947490}, issn = {1932-6203}, abstract = {The National Aeronautics and Space Administration (NASA) has been monitoring the microbial burden of spacecraft since the 1970's Viking missions. Originally culture-based and then focused 16S sequencing techniques were used, but we have now applied whole metagenomic sequencing to a variety of cleanroom samples at the Jet Propulsion Lab (JPL), including the Spacecraft Assembly Facility (SAF) with the goals of taxonomic identification and for functional assignment. Our samples included facility pre-filters, cleanroom vacuum debris, and surface wipes. The taxonomic composition was carried out by three different analysis tools to contrast marker, k-mer, and true alignment approaches. Hierarchical clustering analysis of the data separated vacuum particles from other SAF DNA samples. Vacuum particle samples were the most diverse while DNA samples from the ISO (International Standards Organization) compliant facilities and the SAF were the least diverse; all three were dominated by Proteobacteria. Wipe samples had higher diversity and were predominated by Actinobacteria, including human commensals Cutibacterium acnes and Corynebacterium spp. Taxa identified by the three methods were not identical, supporting the use of multiple methods for metagenome characterization. Likewise, functional annotation was performed using multiple methods. Vacuum particles and SAF samples contained strong signals of the tricarboxylic acid cycle and of amino acid biosynthesis, suggesting that many of the identified microorganisms have the ability to grow in nutrient-limited environments. In total, 18 samples generated high quality metagenome assembled genomes (MAG), which were dominated by Moraxella osloensis or Malassezia restricta. One M. osloensis MAG was assembled into a single circular scaffold and gene annotated. This study includes a rigorous quantitative determination of microbial loads and a qualitative dissection of microbial composition. Assembly of multiple specimens led to greater confidence for the identification of particular species and their predicted functional roles.}, }
@article {pmid36947091, year = {2023}, author = {Yuan, L and Ju, F}, title = {Potential Auxiliary Metabolic Capabilities and Activities Reveal Biochemical Impacts of Viruses in Municipal Wastewater Treatment Plants.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c07800}, pmid = {36947091}, issn = {1520-5851}, abstract = {Viruses influence biogeochemical cycles in oceans, freshwater, soil, and human gut through infection and by modulating virocell metabolism through virus-encoded auxiliary metabolic genes (vAMGs). However, the geographical distribution, potential metabolic function, and engineering significance of vAMGs in wastewater treatment plants (WWTPs) remain to be explored. Here, 752 single-contig viral genomes with high confidence, 510 of which belonged to Caudovirales, were recovered from the activated sludge metagenomes of 32 geographically distributed WWTPs. A total of 101 vAMGs involved in various metabolic pathways were identified, the most common of which were the queuosine biosynthesis genes folE, queD, and queE and the sulfur metabolism gene cysH. Phylogenetic analysis and virus-host relationship prediction revealed the probable evolutionary histories of vAMGs involved in carbon (acpP and prsA), nitrogen (amoC), sulfur (cysH), and phosphate (phoH) metabolism, which potentially mediate microbial carbon and nutrient cycling. Notably, 11 of the 38 (28.3%) vAMGs identified in the metagenomes with corresponding metatranscriptomes were transcriptionally expressed, implying an active functional state. This meta-analysis provides the first broad catalog of vAMGs in municipal WWTPs and how they may assist in the basic physiological reactions of their microbial hosts or nutrient cycling in the WWTPs, and therefore, may have important effects on the engineering of wastewater treatment processes.}, }
@article {pmid36946737, year = {2023}, author = {Castro-Nallar, E and Berríos-Farías, V and Díez, B and Guajardo-Leiva, S}, title = {Seasonal and Spatially Distributed Viral Metagenomes from Comau Fjord (42°S), Patagonia.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0008223}, doi = {10.1128/mra.00082-23}, pmid = {36946737}, issn = {2576-098X}, abstract = {Viruses are key players in marine environments, affecting food webs and biogeochemical cycles. We present 48 viral metagenomes and 5,656 viral operational taxonomic units (vOTUs) from Comau Fjord, Patagonia (42°S), to understand viral-mediated processes in coastal and estuarine waters. These data represent a spatial (35-km transect, two depths) and seasonal (winter and fall) data set.}, }
@article {pmid36946733, year = {2023}, author = {Han, D and Yu, F and Zhang, D and Yang, Q and Xie, M and Yuan, L and Zheng, J and Wang, J and Zhou, J and Xiao, Y and Zheng, S and Chen, Y}, title = {The Real-World Clinical Impact of Plasma mNGS Testing: an Observational Study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0398322}, doi = {10.1128/spectrum.03983-22}, pmid = {36946733}, issn = {2165-0497}, abstract = {Plasma metagenomic next-generation sequencing (mNGS) testing is a promising diagnostic modality for infectious diseases, but its real-world clinical impact is poorly understood. We reviewed patients who had undergone plasma mNGS at a general hospital to evaluate the clinical utility of plasma mNGS testing. A total of 76.9% (113/147) of plasma mNGS tests had a positive result. A total of 196 microorganisms (58) were identified and reported, of which 75.6% (148/196) were clinically relevant. The median stringent mapped read number (SMRN) of clinically relevant organisms was 88 versus 22 for irrelevant organisms (P = 0.04). Based on the clinically adjudicated diagnosis, the positive and negative percent agreements of plasma mNGS testing for identifying a clinically defined infection were 95.2% and 67.4%, respectively. The plasma mNGS results led to a positive impact in 83 (57.1%) patients by diagnosing or ruling out infection and initiating targeted therapy. However, only 32.4% (11/34) of negative mNGS tests showed a positive impact, suggesting that plasma mNGS testing alone may not be a powerful tool to rule out infection in clinical practice. In the subset of 37 patients positive for both plasma mNGS and conventional testing, mNGS identified the pathogen(s) 2 days (IQR = 0.75 to 4.25) earlier than conventional testing. mNGS enables pathogen identification within 24 h, but given that the detection of clinically irrelevant organisms and nearly half of the tests result in no or a negative clinical impact, more clinical practice and studies are required to better understand who and when to test and how to optimally integrate mNGS into the infectious disease diagnostic workup. IMPORTANCE In this study, we show that although plasma mNGS testing significantly improved the detection rate of tested samples, nearly one in four (24.5%, 48/196) mNGS tests reported organisms were not clinically relevant, emphasizing the importance of cautious interpretation and infectious disease consultation. Moreover, based on clinical adjudication, plasma mNGS testing resulted in no or a negative impact in nearly half (43.5%, 64/147) of patients in the current study, indicating that how best to integrate this advanced method into current infectious disease diagnostic frameworks to maximize its clinical utility in real-world practice is an important question. Therefore, recommending plasma mNGS testing as a routine supplement to first-line diagnostic tests for infectious diseases faces great challenges. The decision to conduct mNGS testing should take into account the diagnostic performance, turnaround time and cost-effectiveness of mNGS, as well as the availability of conventional tests.}, }
@article {pmid36946722, year = {2023}, author = {Chung, T and Yan, R and Weller, DL and Kovac, J}, title = {Conditional Forest Models Built Using Metagenomic Data Accurately Predicted Salmonella Contamination in Northeastern Streams.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0038123}, doi = {10.1128/spectrum.00381-23}, pmid = {36946722}, issn = {2165-0497}, abstract = {The use of water contaminated with Salmonella for produce production contributes to foodborne disease burden. To reduce human health risks, there is a need for novel, targeted approaches for assessing the pathogen status of agricultural water. We investigated the utility of water microbiome data for predicting Salmonella contamination of streams used to source water for produce production. Grab samples were collected from 60 New York streams in 2018 and tested for Salmonella. Separately, DNA was extracted from the samples and used for Illumina shotgun metagenomic sequencing. Reads were trimmed and used to assign taxonomy with Kraken2. Conditional forest (CF), regularized random forest (RRF), and support vector machine (SVM) models were implemented to predict Salmonella contamination. Model performance was assessed using 10-fold cross-validation repeated 10 times to quantify area under the curve (AUC) and Kappa score. CF models outperformed the other two algorithms based on AUC (0.86, CF; 0.81, RRF; 0.65, SVM) and Kappa score (0.53, CF; 0.41, RRF; 0.12, SVM). The taxa that were most informative for accurately predicting Salmonella contamination based on CF were compared to taxa identified by ALDEx2 as being differentially abundant between Salmonella-positive and -negative samples. CF and differential abundance tests both identified Aeromonas salmonicida (variable importance [VI] = 0.012) and Aeromonas sp. strain CA23 (VI = 0.025) as the two most informative taxa for predicting Salmonella contamination. Our findings suggest that microbiome-based models may provide an alternative to or complement existing water monitoring strategies. Similarly, the informative taxa identified in this study warrant further investigation as potential indicators of Salmonella contamination of agricultural water. IMPORTANCE Understanding the associations between surface water microbiome composition and the presence of foodborne pathogens, such as Salmonella, can facilitate the identification of novel indicators of Salmonella contamination. This study assessed the utility of microbiome data and three machine learning algorithms for predicting Salmonella contamination of Northeastern streams. The research reported here both expanded the knowledge on the microbiome composition of surface waters and identified putative novel indicators (i.e., Aeromonas species) for Salmonella in Northeastern streams. These putative indicators warrant further research to assess whether they are consistent indicators of Salmonella contamination across regions, waterways, and years not represented in the data set used in this study. Validated indicators identified using microbiome data may be used as targets in the development of rapid (e.g., PCR-based) detection assays for the assessment of microbial safety of agricultural surface waters.}, }
@article {pmid36946719, year = {2023}, author = {Fukushima, K and Matsumoto, Y and Matsuki, T and Saito, H and Motooka, D and Komukai, S and Fukui, E and Yamuchi, J and Nitta, T and Niitsu, T and Abe, Y and Nabeshima, H and Nagahama, Y and Nii, T and Tsujino, K and Miki, K and Kitada, S and Kumanogoh, A and Akira, S and Nakamura, S and Kida, H}, title = {MGIT-seq for the Identification of Nontuberculous Mycobacteria and Drug Resistance: a Prospective Study.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0162622}, doi = {10.1128/jcm.01626-22}, pmid = {36946719}, issn = {1098-660X}, abstract = {Because nontuberculous mycobacterial pulmonary disease is a considerable health burden, a simple and clinically applicable analytical protocol enabling the identification of subspecies and drug-resistant disease is required to determine the treatment strategy. We aimed to develop a simplified workflow consisting only of direct sequencing of mycobacterial growth indicator tube cultures (MGIT-seq). In total, 138 patients were prospectively enrolled between April 2021 and May 2022, and culture-positive MGIT broths were subjected to sequencing using MinION, a portable next-generation sequencer. Sequence analysis was conducted to identify species using core genome multilocus sequence typing and to predict macrolide and amikacin (AMK) resistance based on previously reported mutations in rrl, rrs, and erm(41). The results were compared to clinical tests for species identification and drug susceptibility. A total of 116 patients with positive MGIT cultures were included in the analysis. MGIT-seq yielded 99.1% accuracy in species-level identification and identified 98 isolates (84.5%) at the subspecies level. Macrolide and AMK resistance were detected in 19.4% and 1.9% of Mycobacterium avium complex (MAC) and Mycobacterium abscessus isolates. The predicted macrolide and AMK resistance was consistent with the results of conventional drug susceptibility tests, with specificities of 97.6% and 100.0%, respectively. Direct MGIT-seq has achieved comprehensive identification and drug resistance detection of nontuberculous mycobacteria, which could be applicable to determine the treatment strategy by a single test in clinical practice.}, }
@article {pmid36946508, year = {2023}, author = {Mannan, A and Hoque, MN and Noyon, SH and Hamidullah Mehedi, HM and Foisal, J and Salauddin, A and Rafiqul Islam, SM and Sharmen, F and Tanni, AA and Siddiki, AZ and Tay, A and Siddique, M and Shaminur Rahman, M and Galib, SM and Akter, F}, title = {SARS-CoV-2 infection alters the gut microbiome in diabetes patients: A cross-sectional study from Bangladesh.}, journal = {Journal of medical virology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jmv.28691}, pmid = {36946508}, issn = {1096-9071}, abstract = {Populations of different South Asian nations including Bangladesh reportedly have a high risk of developing diabetes in recent years. This study aimed to investigate the differences in the gut microbiome of COVID-19 positive participants with or without T2DM compared with healthy control subjects. Microbiome data of thirty participants with T2DM were compared with twenty-two age-, sex-, and BMI-matched individuals. Clinical features were recorded while fecal samples were collected aseptically from the participants. Amplicon-based (16S rRNA) metagenome analyses were employed to explore the dysbiosis of gut microbiota and its correlation with genomic and functional features in COVID-19 patients with or without T2DM. Comparing the detected bacterial genera across the sample groups, 98 unique genera were identified, of which nine genera had unique association with COVID-19 T2DM patients. Among different bacterial groups, Shigella (25.0%), Bacteroides (23.45%), and Megamonas (15.90%) had higher mean relative abundances in COVID-19 patients with T2DM. An elevated gut microbiota dysbiosis in T2DM patients with COVID-19 was observed while some metabolic functional changes correlated with bidirectional microbiome dysbiosis between diabetes and non-diabetes humans gut. These results further highlight the possible association of COVID-19 infection that might be linked with alteration of gut microbiome among T2DM patients. This article is protected by copyright. All rights reserved.}, }
@article {pmid36946498, year = {2023}, author = {da Silva, AS and Campos, GM and Giovanetti, M and Zucherato, VS and Lima, ARJ and Santos, EV and Haddad, R and Ciccozzi, M and Alcantara, LCJ and Elias, MC and Sampaio, SC and Covas, DT and Kashima, S and Slavov, SN}, title = {VIRAL METAGENOMICS UNVEILS MW (MALAWI) POLYOMAVIRUS INFECTION IN BRAZILIAN PEDIATRIC PATIENTS WITH ACUTE RESPIRATORY DISEASE.}, journal = {Journal of medical virology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jmv.28688}, pmid = {36946498}, issn = {1096-9071}, abstract = {Viral metagenomics has been extensively applied for the identification of emerging or poorly characterized viruses. In this study, we applied metagenomics for the identification of viral infections among pediatric patients with acute respiratory disease but who tested negative for SARS-CoV-2. Twelve pools composed of 8 nasopharyngeal specimens were submitted to viral metagenomics. Surprisingly, in two of the pools, we identified reads belonging to the poorly characterized Malawi polyomavirus (MWPyV). Then, the samples composing the positive pools were individually tested using qPCR for identification of the MWPyV index cases. MWPyV positive samples were also submitted to respiratory virus panel testing due to the metagenomic identification of different clinically important viruses. Of note, MWPyV positive samples tested also positive for respiratory syncytial virus types A and B. In this study, we retrieved two complete MWPyV genome sequences from the index samples that were submitted to phylogenetic inference to investigate their viral origin. Our study represents the first molecular and genomic characterization of MWPyV obtained from pediatric patients in South America. The detection of MWPyV in acutely infected infants suggests that this virus might participate (co-participate) in cases of respiratory symptoms. Nevertheless, future studies based on testing of a larger number of clinical samples and MWPyV complete genomes appear to be necessary to elucidate if this emerging polyomavirus might be clinically important. This article is protected by copyright. All rights reserved.}, }
@article {pmid36946423, year = {2023}, author = {Sivapornnukul, P and Chitcharoen, S and Sawaswong, V and Tachaboon, S and Dinhuzen, J and Srisawat, N and Payungporn, S}, title = {Comparison of circulating bacterial profiles between mild and severe COVID-19 patients.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {}, number = {}, pages = {15353702231157931}, doi = {10.1177/15353702231157931}, pmid = {36946423}, issn = {1535-3699}, abstract = {Recent reports revealed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients can develop bacteremia; however, the circulating bacterial profile is not well studied. Therefore, this study has aimed to investigate circulating bacterial profile in mild (n = 15) and severe (n = 13) SARS-CoV-2-infected patients as well as healthy controls (n = 10), using 16S rDNA (V4) sequencing approach. The alpha diversity indexes and Bray-Curtis dissimilarity matrix revealed that the bacterial profiles between the two conditions are significantly different. Correspondingly, the relative abundance indicates that the predominant bacterial phylum in both conditions was Proteobacteria. At genus level, the dominant bacterial genera in the mild patients belonged to Sphingomonas, Stenotrophomonas, and Achromobacter, while bacterial genera belonging to Enhydrobacter, Comamonas, and Acinetobacter were dominant in the severe patients. Furthermore, Linear discriminant analysis (LDA) Effect Size (LEfSe). revealed that Stenotrophomonas, Delftia, Achromobacter, and Neisseria were enriched in the mild condition, while Agrobacterium, Comamonas, Pseudomonas, Corynebacterium, Alkaliphilus, and Kocuria were enriched in the severe patients. These results revealed a distinct circulating bacterial profile in the mild and severe SARS-CoV-2-infected patients, which may provide an insight for further therapeutic strategy.}, }
@article {pmid36945965, year = {2023}, author = {Konak, HE and Erden, A and Armağan, B and Güven, SC and Apaydın, H and Dağlı, PA and Uzun, Y and Kaygısız, M and Küçükşahin, O and Omma, A}, title = {Effects of breast milk on Behçet's disease clinical features.}, journal = {Turkish journal of medical sciences}, volume = {53}, number = {1}, pages = {121-129}, pmid = {36945965}, issn = {1303-6165}, abstract = {BACKGROUND: The etiology of Behçet's disease (BD) is not clearly known, however, abnormal activity in T helper (Th) 1, Th 17, and regulatory T cells (Treg) has critical importance in pathogenesis. It has been shown that the intestinal microbiome can be effective in the modulation of these immune abnormalities in BD patients. Breastfeeding increases the maturation of the infant's intestinal permeability by affecting the newborn's immature intestinal microbiome and metagenome. We aimed to examine the effects of breastfeeding on disease related symptoms, organ involvements and course of the disease in BD patients.<br><br>METHODS: This study was designed as a cross-sectional study in Ankara City Hospital rheumatology clinic between December 2021 and March 2022. Patients who were diagnosed with BD by meeting the criteria of the 'International Study Group' and whose information we could access by agreeing to participate in the study were enrolled. The mothers of the patients were also contacted and asked whether these patients were breastfed, the duration of breastfeeding, and the mode of birth. Demographic and clinical data of the patients, comorbid diseases, and drugs used for BD were collected from the records in the hospital database. The presence of sacroiliitis in patients was evaluated with sacroiliac X-ray and/or magnetic resonance imaging (MRI), which was requested because of low back pain symptoms and only patients with previous sacroiliac imaging for low back pain were included in the study. BD-related organ damage was measured by the Vasculitis Damage Index (VDI) and Beh&#xe7;et's syndrome Overall Damage Index (BODI) scores.<br><br>RESULTS: : A total of 304 patients were included in the study. The percentage of patients who were reported to have ever breastfed (median duration (IQR): 12(12) months, 33.5% < 6 months, 66.4% &#x2265; 6 months, and 59.6% &#x2265; 12 months) is 92%. When the breastfed and nonbreastfed patients were compared, 6.8% of the breastfed patients needed TNF-i against 18.2% of the nonbreastfed patients (p = 0.052). While the rate of having at least one comorbidity was 26.4% for those who were breastfed, this rate was 50% for those who had never been breastfed. When the organ and system involvements of the patients were compared, the incidence of sacroiliitis was statistically significantly higher in the nonbreastfed group (p = 0.025). Patients who were breastfed for less than 6 months were diagnosed with BD at an earlier age than those who were breastfed for more than 6 months, and those who were breastfed for less than 12 months compared to those who were breastfed for more than 12 months (respectively, p = 0.039, p = 0.035).<br><br>DISCUSSION: Our results imply that history of breastfeeding may have some positive effects on the course of the disease in BD patients.}, }
@article {pmid36945677, year = {2022}, author = {Fomsgaard, AS and Rasmussen, M and Spiess, K and Fomsgaard, A and Belsham, GJ and Fonager, J}, title = {Improvements in metagenomic virus detection by simple pretreatment methods.}, journal = {Journal of clinical virology plus}, volume = {2}, number = {4}, pages = {100120}, pmid = {36945677}, issn = {2667-0380}, abstract = {Early detection of pathogens at the point of care helps reduce the threats to human and animal health from emerging pathogens. Initially, the disease-causing agent will be unknown and needs to be identified; this often requires specific laboratory facilities. Here we describe the development of an unbiased detection assay for RNA and DNA viruses using metagenomic Nanopore sequencing and simple methods that can be transferred into a field setting. Human clinical samples containing the RNA virus SARS-CoV-2 or the DNA viruses human papillomavirus (HPV) and molluscum contagiosum virus (MCV) were used as a test of concept. Firstly, the virus detection potential was optimized by investigating different pretreatments for reducing non-viral nucleic acid components. DNase I pretreatment followed by filtration increased the proportion of SARS-CoV-2 sequenced reads > 500-fold compared with no pretreatments. This was sufficient to achieve virus detection with high confidence and allowed variant identification. Next, we tested individual SARS-CoV-2 samples with various viral loads (measured as CT-values determined by RT-qPCR). Lastly, we tested the assay on clinical samples containing the DNA virus HPV and co-infection with MCV to show the assay's detection potential for DNA viruses. This protocol is fast (same day results). We hope to apply this method in other settings for point of care detection of virus pathogens, thus eliminating the need for transport of infectious samples, cold storage and a specialized laboratory.}, }
@article {pmid36945612, year = {2023}, author = {Wang, Y and Sun, Y and Li, X and Chen, R and Li, W and Ji, L and Zhao, Q and Ji, L and Yang, S and Zhang, W}, title = {Molecular detection and characterization of three novel parvoviruses belonging to two different subfamilies in zoo birds.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-2593815/v1}, pmid = {36945612}, abstract = {Birds carry a large number of viruses that may cause diseases in animals or human. At present, virome of zoo birds are limited. In this study, using viral metagenomics method, we investigated the feces virome of zoo birds collected from a zoo of Nanjing, Jiangsu Province, China. Three novel parvoviruses were obtained and characterized. The genome of the three viruses are 5,909 bp, 4,411 bp and 4,233 bp in length respectively which encoded four or five ORFs. Phylogenetic analysis indicated that these three novel parvoviruses clustered with other strains formed three different clades. Pairwise comparison of NS1 amino acid sequences showed that Bir-01-1 shared 44.30%-74.92% aa sequence identity with other parvoviruses belonging to the genus Aveparvovirus, while Bir-03-1 and Bir-04-1 had lower than 66.87% and 53.09% aa sequence identity with other parvoviruses belonging to the genus Chaphamaparvovirus. These three viruses were identified as three novel species of the genus Aveparvovirus and Chaphamaparvovirus respectively basing on the species demarcation criteria of parvovirus. Our findings broaden the knowledge of the genetic diversity of parvovirus and provide epidemiological data for the outbreak of potential bird’s parvovirus disease.}, }
@article {pmid36945052, year = {2023}, author = {Wang, Y and Zhang, Y and Hu, Y and Liu, L and Liu, SJ and Zhang, T}, title = {Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {56}, pmid = {36945052}, issn = {2049-2618}, abstract = {BACKGROUND: Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution and complex associations with bacterial hosts, genetic and biological features of CPR bacteria in low-nutrient environments have received increasing attention. However, CPR bacteria in wastewater treatment systems remain poorly understood. We utilized genome-centric metagenomics to answer how CPR communities shift over 11 years and what kind of ecological roles they act in an activated sludge system.<br><br>RESULTS: We found that approximately 9% (135) of the 1,526 non-redundant bacterial and archaeal metagenome-assembled genomes were affiliated with CPR. CPR bacteria were consistently abundant with a relative abundance of up to 7.5% in the studied activated sludge system. The observed striking fluctuations in CPR community compositions and the limited metabolic and biosynthetic capabilities in CPR bacteria collectively revealed the nature that CPR dynamics may be directly determined by the available hosts. Similarity-based network analysis further confirmed the broad bacterial hosts of CPR lineages. The proteome contents of activated sludge-associated CPR had a higher similarity to those of environmental-associated CPR than to those of human-associated ones. Comparative genomic analysis observed significant enrichment of genes for oxygen stress resistance in activated sludge-associated CPR bacteria. Furthermore, genes for carbon cycling and horizontal gene transfer were extensively identified in activated sludge-associated CPR genomes.<br><br>CONCLUSIONS: These findings highlight the presence of specific host interactions among CPR lineages in activated sludge systems. Despite the lack of key metabolic pathways, these small, yet abundant bacteria may have significant involvements in biogeochemical cycling and bacterial evolution in activated sludge systems. Video Abstract.}, }
@article {pmid36944808, year = {2023}, author = {Schotte, U and Binder, A and Goller, KV and Faulde, M and Ruhl, S and Sauer, S and Schlegel, M and Teifke, JP and Ulrich, RG and Wylezich, C}, title = {Field survey and molecular characterization of apicomplexan parasites in small mammals from military camps in Afghanistan.}, journal = {Parasitology research}, volume = {}, number = {}, pages = {}, pmid = {36944808}, issn = {1432-1955}, abstract = {Small mammals are an important reservoir for causative agents of numerous infectious diseases, including zoonotic and vector-borne diseases. The occurrence of these pathogens represents a regional but permanent threat for humans and animals in general and might especially weaken military personnel and companion animals in abroad missions. In our study, small mammals collected in military camps in Afghanistan (Feyzabad, Mazar-e Sharif, and Kunduz) were investigated for the presence of apicomplexans using histopathology and molecular methods. For this purpose, well-established and newly developed real-time PCR assays were applied. A high prevalence was detected not only in house mice (Mus musculus), but also in shrews (Crocidura cf. suaveolens) and grey dwarf hamsters (Cricetulus migratorius). The molecular characterization based on the 18S rRNA gene revealed a close relationship to a cluster of Hepatozoon sp. detected in voles of the genus Microtus. Hepatozoon canis DNA was detected in one house mouse as well as in two Rhipicephalus ticks from a dog puppy. In addition, around 5% of the house mice were found to be infected with far related adeleorinids showing the highest sequence identity of 91.5% to Klossiella equi, the only published Klossiella sequence at present. For their better phylogenetic characterization, we conducted metagenomics by sequencing of two selected samples. The resulting 18S rRNA gene sequences have a length of about 2400 base pairs including an insertion of about 500 base pairs and are 100% identical to each other. Histopathology together with organ tropism and detection rates verified this sequence as of Klossiella muris. In conclusion, we documented naturally occurring protozoan stages and the additional taxonomic characterization of a well-known commensal in mice by applying a combination of different approaches. The study is of medical, social, and biological importance for ensuring human and animal health in military camps and also stresses the required awareness for the potential risk of zoonoses.}, }
@article {pmid36943918, year = {2023}, author = {Kharofa, J and Haslam, D and Wilkinson, R and Weiss, A and Patel, S and Wang, K and Esslinger, H and Olowokure, O and Sohal, D and Wilson, G and Ahmad, S and Apewokin, S}, title = {Analysis of the fecal metagenome in long-term survivors of pancreas cancer.}, journal = {Cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/cncr.34748}, pmid = {36943918}, issn = {1097-0142}, support = {5K08CA237735/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: The 5-year overall survival of pancreas adenocarcinoma (PCa) remains less than 10%. Clinical and tumor genomic characteristics have not differentiated PCa long-term survivors (LTSs) from unselected patients. Preclinical studies using fecal transplant experiments from LTSs of PCa have revealed delayed tumor growth through unknown mechanisms involving the fecal microbiota. However, features of the fecal microbiome in patients with long-term survival are not well described.<br><br>METHODS: In this cross-sectional study, comprehensive shotgun metagenomics was performed on stool from PCa patients with long-term survival (n&#xa0;=&#xa0;16). LTS was defined as >4&#xa0;years from pancreatectomy and all therapy without recurrence. LTSs were compared to control patients with PCa who completed pancreatectomy and chemotherapy (n&#xa0;=&#xa0;8). Stool was sequenced using an Illumina NextSeq500. Statistical analyses were performed in R with MicrobiomeSeq and Phyloseq for comparison of LTSs and controls.<br><br>RESULTS: All patients underwent pancreatectomy and chemotherapy before sample donation. The median time from pancreatectomy of 6&#xa0;years (4-14&#xa0;years) for LTSs without evidence of disease compared to a median disease-free survival of 1.8&#xa0;years from pancreatectomy in the control group. No differences were observed in overall microbial diversity for LTSs and controls using Shannon/Simpson indexes. Significant enrichment of species relative abundance was observed in LTSs for the Ruminococacceae family specifically Faecalibacterium prausnitzii species as well as Akkermansia mucinophilia species.<br><br>CONCLUSIONS: Stool from patients cured from PCa has more relative abundance of Faecalibacterium prausnitzii and Akkermansia mucinophilia. Additional studies are needed to explore potential mechanisms by which the fecal microbiota may influence survival in PCa.<br><br>PLAIN LANGUAGE SUMMARY: Although pancreatic cancer treatments have improved, the number of long-term survivors has remained stagnant with a 5-year overall survival estimate of 9%. Emerging evidence suggests that microbes within the gastrointestinal tract can influence cancer response through activation of the immune system. In this study, we profiled the stool microbiome in long-term survivors of pancreas cancer and controls. Several enriched species previously associated with enhanced tumor immune response were observed including Faecalibacterium prausnitzii and Akkermansia mucinophilia. These findings warrant additional study assessing mechanisms by which the fecal microbiota may enhance pancreatic cancer immune response.}, }
@article {pmid36943133, year = {2023}, author = {Kronen, M and Vázquez-Campos, X and Wilkins, MR and Lee, M and Manefield, MJ}, title = {Evidence for a Putative Isoprene Reductase in Acetobacterium wieringae.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0011923}, doi = {10.1128/msystems.00119-23}, pmid = {36943133}, issn = {2379-5077}, abstract = {Recent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome-assembled genome (MAG) of the most abundant (89% relative abundance) lineage in the enrichment, Acetobacterium wieringae, was obtained. Comparative proteogenomics and reverse transcription-PCR (RT-PCR) identified a putative five-gene operon from the A. wieringae MAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 × HypA, HypB), and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, flavin adenine dinucleotide (FAD), two pairs of canonical [4Fe-4S] clusters, and a putative iron-sulfur cluster site in a Cys6-bonding environment. Well-studied Acetobacterium strains, such as A. woodii DSM 1030, A. wieringae DSM 1911, or A. malicum DSM 4132, do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase (~47 to 49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across the Firmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, Bacteroidetes, and Proteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons. IMPORTANCE Isoprene was recently shown to act as an electron acceptor for a homoacetogenic bacterium. The focus of this study is the molecular basis for isoprene reduction. By comparing a genome from our isoprene-reducing enrichment culture, dominated by Acetobacterium wieringae, with genomes of other Acetobacterium lineages that do not reduce isoprene, we shortlisted candidate genes for isoprene reduction. Using comparative proteogenomics and reverse transcription-PCR we have identified a putative five-gene operon encoding an oxidoreductase referred to as putative isoprene reductase.}, }
@article {pmid36943059, year = {2023}, author = {Durán-Viseras, A and Sánchez-Porro, C and Viver, T and Konstantinidis, KT and Ventosa, A}, title = {Discovery of the Streamlined Haloarchaeon Halorutilus salinus, Comprising a New Order Widespread in Hypersaline Environments across the World.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0119822}, doi = {10.1128/msystems.01198-22}, pmid = {36943059}, issn = {2379-5077}, abstract = {The class Halobacteria is one of the most diverse groups within the Euryarchaeota phylum, whose members are ubiquitously distributed in hypersaline environments, where they often constitute the major population. Here, we report the discovery and isolation of a new halophilic archaeon, strain F3-133[T] exhibiting ≤86.3% 16S rRNA gene identity to any previously cultivated archaeon, and, thus, representing a new order. Analysis of available 16S rRNA gene amplicon and metagenomic data sets showed that the new isolate represents an abundant group in intermediate-to-high salinity ecosystems and is widely distributed across the world. The isolate presents a streamlined genome, which probably accounts for its ecological success in nature and its fastidious growth in culture. The predominant osmoprotection mechanism appears to be the typical salt-in strategy used by other haloarchaea. Furthermore, the genome contains the complete gene set for nucleotide monophosphate degradation pathway through archaeal RuBisCO, being within the first halophilic archaea representatives reported to code this enzyme. Genomic comparisons with previously described representatives of the phylum Euryarchaeota were consistent with the 16S rRNA gene data in supporting that our isolate represents a novel order within the class Halobacteria for which we propose the names Halorutilales ord. nov., Halorutilaceae fam. nov., Halorutilus gen. nov. and Halorutilus salinus sp. nov. IMPORTANCE The discovery of the new halophilic archaeon, Halorutilus salinus, representing a novel order, family, genus, and species within the class Halobacteria and phylum Euryarchaeota clearly enables insights into the microbial dark matter, expanding the current taxonomical knowledge of this group of archaea. The in-depth comparative genomic analysis performed on this new taxon revealed one of the first known examples of an Halobacteria representative coding the archaeal RuBisCO gene and with a streamlined genome, being ecologically successful in nature and explaining its previous non-isolation. Altogether, this research brings light into the understanding of the physiology of the Halobacteria class members, their ecological distribution, and capacity to thrive in hypersaline environments.}, }
@article {pmid36943058, year = {2023}, author = {Rao, YZ and Li, YX and Li, ZW and Qu, YN and Qi, YL and Jiao, JY and Shu, WS and Hua, ZS and Li, WJ}, title = {Metagenomic Discovery of "Candidatus Parvarchaeales"-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0125222}, doi = {10.1128/msystems.01252-22}, pmid = {36943058}, issn = {2379-5077}, abstract = {"Candidatus Parvarchaeales" microbes, representing a DPANN archaeal group with limited metabolic potential and reliance on hosts for their growth, were initially found in acid mine drainage (AMD). Due to the lack of representatives, however, their ecological roles and adaptation to extreme habitats such as AMD as well as how they diverge across the lineage remain largely unexplored. By applying genome-resolved metagenomics, 28 Parvarchaeales-associated metagenome-assembled genomes (MAGs) representing two orders and five genera were recovered. Among them, we identified three new genera and proposed the names "Candidatus Jingweiarchaeum," "Candidatus Haiyanarchaeum," and "Candidatus Rehaiarchaeum," with the former two belonging to a new order, "Candidatus Jingweiarchaeales." Further analyses of the metabolic potentials revealed substantial niche differentiation between Jingweiarchaeales and Parvarchaeales. Jingweiarchaeales may rely on fermentation, salvage pathways, partial glycolysis, and the pentose phosphate pathway (PPP) for energy conservation reservation, while the metabolic potentials of Parvarchaeales might be more versatile. Comparative genomic analyses suggested that Jingweiarchaeales favor habitats with higher temperatures and that Parvarchaeales are better adapted to acidic environments. We further revealed that the thermal adaptation of these lineages, especially Haiyanarchaeum, might rely on genomic features such as the usage of specific amino acids, genome streamlining, and hyperthermophile featured genes such as rgy. Notably, the adaptation of Parvarchaeales to acidic environments was possibly driven by horizontal gene transfer (HGT). The reconstruction of ancestral states demonstrated that both may have originated from thermal and neutral environments and later spread to mesothermal and acidic environments. These evolutionary processes may also be accompanied by adaptation to oxygen-rich environments via HGT. IMPORTANCE "Candidatus Parvarchaeales" microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments. By the discovery of potential new order-level lineages, "Ca. Jingweiarchaeales," and in-depth comparative genomic analysis, we unveiled the functional differentiation of these lineages. Furthermore, we show that the adaptation of these lineages to high-temperature and acidic environments was driven by different strategies, with the former relying more on genomic characteristics such as genome streamlining and amino acid compositions and the latter relying more on the acquisition of genes associated with acid tolerance. Finally, by the reconstruction of the ancestral states of the optimal growth temperature (OGT) and isoelectric point (pI), we showed the potential evolutionary process of Parvarchaeales-related lineages with regard to the shift from the high-temperature environment of their common ancestors to low-temperature (potentially acidic) environments.}, }
@article {pmid36928772, year = {2023}, author = {Zhao, X and Guo, Y and Kang, L and Yin, C and Bi, A and Xu, D and Zhang, Z and Zhang, J and Yang, X and Xu, J and Xu, S and Song, X and Zhang, M and Li, Y and Kear, P and Wang, J and Liu, Z and Fu, X and Lu, F}, title = {Population genomics unravels the Holocene history of bread wheat and its relatives.}, journal = {Nature plants}, volume = {9}, number = {3}, pages = {403-419}, pmid = {36928772}, issn = {2055-0278}, mesh = {Animals ; Humans ; *Genome, Plant ; *Triticum/genetics ; Metagenomics ; Bread ; Europe ; }, abstract = {Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accessions, we found that bread wheat originated from the southwest coast of the Caspian Sea and underwent a slow speciation process, lasting ~3,300 yr owing to persistent gene flow from its relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia and East Asia ~7,000 to ~5,000 yr ago, shaping a diversified but occasionally convergent adaptive landscape in novel environments. By contrast, the cultivated relatives of bread wheat experienced a population decline by ~82% over the past ~2,000 yr due to the food choice shift of humans. Further biogeographical modelling predicted a continued population shrinking of many bread wheat relatives in the coming decades because of their vulnerability to the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to enhance global wheat production.}, }
@article {pmid36943045, year = {2023}, author = {Lu, J and Zeng, L and Holford, P and Beattie, GAC and Wang, Y}, title = {Discovery of Brassica Yellows Virus and Porcine Reproductive and Respiratory Syndrome Virus in Diaphorina citri and Changes in Virome Due to Infection with 'Ca. L. asiaticus'.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0499622}, doi = {10.1128/spectrum.04996-22}, pmid = {36943045}, issn = {2165-0497}, abstract = {Detection of new viruses or new virus hosts is essential for the protection of economically important agroecosystems and human health. Increasingly, metatranscriptomic data are being used to facilitate this process. Such data were obtained from adult Asian citrus psyllids (ACP) (Diaphorina citri Kuwayama) that fed solely on mandarin (Citrus ×aurantium L.) plants grafted with buds infected with 'Candidatus Liberibacter asiaticus' (CLas), a phloem-limited bacterium associated with the severe Asian variant of huanglongbing (HLB), the most destructive disease of citrus. Brassica yellows virus (BrYV), the causative agent of yellowing or leafroll symptoms in brassicaceous plants, and its associated RNA (named as BrYVaRNA) were detected in ACP. In addition, the porcine reproductive and respiratory syndrome virus (PRRSV), which affects pigs and is economically important to pig production, was also found in ACP. These viruses were not detected in insects feeding on plants grafted with CLas-free buds. Changes in the concentrations of insect-specific viruses within the psyllid were caused by coinfection with CLas. IMPORTANCE The cross transmission of pathogenic viruses between different farming systems or plant communities is a major threat to plants and animals and, potentially, human health. The use of metagenomics is an effective approach to discover viruses and vectors. Here, we collected buds from the CLas-infected and CLas-free mandarin (Citrus ×aurantium L. [Rutaceae: Aurantioideae: Aurantieae]) trees from a commercial orchard and grafted them onto CLas-free mandarin plants under laboratory conditions. Through metatranscriptome sequencing, we first identified the Asian citrus psyllids feeding on plants grafted with CLas-infected buds carried the plant pathogen, brassica yellows virus and its associated RNA, and the swine pathogen, porcine reproductive and respiratory syndrome virus. These discoveries indicate that both viruses can be transmitted by grafting and acquired by ACP from CLas+ mandarin seedlings.}, }
@article {pmid36941739, year = {2023}, author = {Li, F and Wang, J and Chen, C and Yang, H and Man, R and Yu, S}, title = {Otomastoiditis Caused by Nocardia Farcinica: A Case Report and Literature Review.}, journal = {Ear, nose, &amp; throat journal}, volume = {}, number = {}, pages = {1455613231165166}, doi = {10.1177/01455613231165166}, pmid = {36941739}, issn = {1942-7522}, abstract = {Nocardia farcinica usually infects people with impaired immune status and usually manifests in the lungs. Otomastoiditis caused by Nocardia infection is extremely rare, with only 4 cases reported to date. This report describes a case of otomastoid N. farcinica infection in an immunocompetent patient. The case was a 10-month-old immunocompetent infant who presented with an approximately 3-month history of right ear discharge for which treatment with various antibiotics had not resulted in significant improvement. Multiple cultures of secretions and pathologic examination failed to identify the causative organism. The patient then underwent right mastoidectomy. Finally, metagenomic next-generation sequencing identified the pathogen to be N. farcinica. The patient was infection-free at the 6-month follow-up but had developed labyrinthitis ossificans. Otomastoid Nocardia infection has characteristic clinical features, namely, formation of a large amount of granulation tissue and coexistence of bone destruction and new bone formation. Traditionally, Nocardia is challenging to diagnose. Metagenomic next-generation sequencing of lesions is helpful. Complete local debridement and free drainage are key to treatment.}, }
@article {pmid36941650, year = {2023}, author = {Lu, X and Zhu, R and Dai, Z}, title = {Characterization of a novel papillomavirus identified from a whale (Delphinapterus leucas) pharyngeal metagenomic library.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {48}, pmid = {36941650}, issn = {1743-422X}, abstract = {Here, using viral metagenomic method, a novel whale papillomavirus (temporarily named wPV, GenBank accession number OP856597) was discovered in a whale (Delphinapterus leucas) pharyngeal metagenomic library. The complete genome size of wPV is 7179 bp, with GC content of 54.4% and a nucleotide composition of 23.4% A, 22.3% T, 28.4% G, and 25.9% C. The viral genome has a typical papillomavirus organization pattern, and five ORFs were predicted, including two late genes encoding L1 and L2, and three early genes encoding E1, E2, and E6. Pairwise sequence comparison and phylogenetic analysis based on the L1 gene sequence indicated that wPV may be a novel species within genus Dyodeltapapillomavirus. In addition, the E2 region of wPV was predicted to have a potential recombination event. The discovery of this novel papillomavirus increases our understanding of the viral ecology of marine mammals, providing insights into possible future infectious diseases.}, }
@article {pmid36941644, year = {2023}, author = {Neyton, LPA and Langelier, CR and Calfee, CS}, title = {Metagenomic Sequencing in the ICU for Precision Diagnosis of Critical Infectious Illnesses.}, journal = {Critical care (London, England)}, volume = {27}, number = {1}, pages = {90}, pmid = {36941644}, issn = {1466-609X}, abstract = {This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2023. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2023 . Further information about the Annual Update in Intensive Care and Emergency Medicine is available from https://link.springer.com/bookseries/8901 .}, }
@article {pmid36941307, year = {2023}, author = {Kruasuwan, W and Jenjaroenpun, P and Arigul, T and Chokesajjawatee, N and Leekitcharoenphon, P and Foongladda, S and Wongsurawat, T}, title = {Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4540}, pmid = {36941307}, issn = {2045-2322}, abstract = {The market for the application of probiotics as a livestock health improvement supplement has increased in recent years. However, most of the available products are quality-controlled using low-resolution techniques and un-curated databases, resulting in misidentification and incorrect product labels. In this work, we deployed two workflows and compared results obtained by full-length 16S rRNA genes (16S) and metagenomic (Meta) data to investigate their reliability for the microbial composition of both liquid and solid forms of animal probiotic products using Oxford Nanopore long-read-only (without short-read). Our result revealed that 16S amplicon data permits to detect the bacterial microbiota even with the low abundance in the samples. Moreover, the 16S approach has the potential to provide species-level resolution for prokaryotes but not for assessing yeast communities. Whereas, Meta data has more power to recover of high-quality metagenome-assembled genomes that enables detailed exploration of both bacterial and yeast populations, as well as antimicrobial resistance genes, and functional genes in the population. Our findings clearly demonstrate that implementing these workflows with long-read-only monitoring could be applied to assessing the quality and safety of probiotic products for animals and evaluating the quality of probiotic products on the market. This would benefit the sustained growth of the livestock probiotic industry.}, }
@article {pmid36940870, year = {2023}, author = {Wang, B and Zhang, L and Shi, J and Su, Y and Wu, D and Xie, B}, title = {Genome-centric metagenomics revealed functional traits in high-solids anaerobic co-digestion of restaurant food waste, household food waste and rice straw.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {128926}, doi = {10.1016/j.biortech.2023.128926}, pmid = {36940870}, issn = {1873-2976}, abstract = {High-solids anaerobic co-digestion (HS-AcoD) of food waste (FW) and other organic wastes is an effective option to improve the biogas production and system stability compared to mono-digestion. However, the clean and sustainable HS-AcoD strategy for FW and associated microbial functional traits have not been well explored. Here, HS-AcoD of restaurant food waste (RFW), household food waste (HFW) and rice straw (RS) were performed. Results showed that the maximum synergy index (SI) of 1.28 were achieved when the volatile solids ratio of RFW, HFW and RS was 0.45:0.45:0.1. HS-AcoD alleviated the acidification process by regulating metabolism associated with hydrolysis and volatile fatty acids formation. The synergistic relationship between syntrophic bacteria and Methanothrix sp., and the enhanced metabolic capacity associated with the acetotrophic and hydrogenotrophic pathways dominated by Methanothrix sp., provided a further explanation of the synergistic mechanism. These findings advance the knowledge about microbial mechanisms underlying the synergistic effect of HS-AcoD.}, }
@article {pmid36940753, year = {2023}, author = {Stiernborg, M and Debelius, JW and Yang, LL and Skott, E and Millischer, V and Giacobini, M and Melas, PA and Boulund, F and Lavebratt, C}, title = {Bacterial gut microbiome differences in adults with ADHD and in children with ADHD on psychostimulant medication.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2023.03.012}, pmid = {36940753}, issn = {1090-2139}, abstract = {Recent evidence suggests that there is a link between neurodevelopmental disorders, such as attention deficit hyperactivity disorder (ADHD), and the gut microbiome. However, most studies to date have had low sample sizes, have not investigated the impact of psychostimulant medication, and have not adjusted for potential confounders, including body mass index, stool consistency and diet. To this end, we conducted the largest, to our knowledge, fecal shotgun metagenomic sequencing study in ADHD, with 147 well-characterized adult and child patients. For a subset of individuals, plasma levels of inflammatory markers and short-chain fatty acids were also measured. In adult ADHD patients (n=84), compared to controls (n=52), we found a significant difference in beta diversity both regarding bacterial strains (taxonomic) and bacterial genes (functional). In children with ADHD (n=63), we found that those on psychostimulant medication (n=33 on medication vs. n=30 not on medication) had (i) significantly different taxonomic beta diversity, (ii) lower functional and taxonomic evenness, (iii) lower abundance of the strain Bacteroides stercoris CL09T03C01 and bacterial genes encoding an enzyme in vitamin B12 synthesis, and (iv) higher plasma levels of vascular inflammatory markers sICAM-1 and sVCAM-1. Our study continues to support a role for the gut microbiome in neurodevelopmental disorders and provides additional insights into the effects of psychostimulant medication. However, additional studies are needed to replicate these findings and examine causal relationships with the disorder.}, }
@article {pmid36940534, year = {2023}, author = {Andersen, VD and Møller, FD and Jensen, MS and Aarestrup, FM and Vigre, H}, title = {The quantitative effect of antimicrobial usage in Danish pig farms on the abundance of antimicrobial resistance genes in slaughter pigs.}, journal = {Preventive veterinary medicine}, volume = {214}, number = {}, pages = {105899}, doi = {10.1016/j.prevetmed.2023.105899}, pmid = {36940534}, issn = {1873-1716}, abstract = {Research has long established the connection between antimicrobial use (AMU) and antimicrobial resistance (AMR) in production animals, and shown that the ceasing of AMU reduces AMR. Our previous study of Danish slaughter-pig production found a quantitative relationship between lifetime AMU and abundance of antimicrobial resistance genes (ARGs). This study aimed to generate further quantitative knowledge on how changes in AMU in farms influence the abundance of ARGs both with immediate effect and over time. The study included 83 farms that were visited from 1 to 5 times. From each visit, a pooled faecal sample was produced. The abundance of ARGs was obtained by metagenomics. We used two-level linear mixed models for estimating the effect of AMU on the abundance of ARGs against six antimicrobial classes. The lifetime AMU of each batch was calculated from usage during their three rearing periods; as piglets, weaners and slaughter pigs (rearing pathway). AMU at farm level was estimated as the mean lifetime AMU of the sampled batches from each farm. At batch level, AMU was measured as the deviation between the batch-specific lifetime AMU and the general mean lifetime AMU at the farm. For peroral tetracycline and macrolide use there was a significant quantitative linear effect on the abundance of ARGs in batches within individual farms, indicating an immediate effect of changed AMU from batch to batch within farms. These estimated effects between batches within farms were approximately 1/2-1/3 of the effect estimated between farms. For all antimicrobial classes, the effect of the mean farm-level AMU and the abundance of ARGs present in the faeces of slaughter pigs was significant. This effect was identified only for peroral use, except for lincosamides, where the effect was for parenteral use. The results also indicated that the abundance of ARGs against a specific antimicrobial class also increased by the peroral usage of one or several other antimicrobial classes, except for ARGs against beta-lactams. These effects were generally lower than the AMU effect of the specific antimicrobial class. Overall, the farm peroral mean lifetime AMU affected the abundance of ARGs at antimicrobial class level and abundance of ARGs of other classes. However, the difference of AMU of the slaughter-pig batches affected only the abundance of ARGs at the same antimicrobial class level in the same antimicrobial class. The results do not exclude that parenteral usage of antimicrobials may have an effect on the abundance of ARGs.}, }
@article {pmid36939866, year = {2023}, author = {Malard, LA and Bergk-Pinto, B and Layton, R and Vogel, TM and Larose, C and Pearce, DA}, title = {Snow Microorganisms Colonise Arctic Soils Following Snow Melt.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {36939866}, issn = {1432-184X}, abstract = {Arctic soils are constantly subjected to microbial invasion from either airborne, marine, or animal sources, which may impact local microbial communities and ecosystem functioning. However, in winter, Arctic soils are isolated from outside sources other than snow, which is the sole source of microorganisms. Successful colonisation of soil by snow microorganisms depends on the ability to survive and compete of both, the invading and resident community. Using shallow shotgun metagenome sequencing and amplicon sequencing, this study monitored snow and soil microbial communities throughout snow melt to investigate the colonisation process of Arctic soils. Microbial colonisation likely occurred as all the characteristics of successful colonisation were observed. The colonising microorganisms originating from the snow were already adapted to the local environmental conditions and were subsequently subjected to many similar conditions in the Arctic soil. Furthermore, competition-related genes (e.g. motility and virulence) increased in snow samples as the snow melted. Overall, one hundred potentially successful colonisers were identified in the soil and, thus, demonstrated the deposition and growth of snow microorganisms in soils during melt.}, }
@article {pmid36939224, year = {2023}, author = {Ghadigaonkar, D and Rath, A}, title = {Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {193}, pages = {}, doi = {10.3791/63934}, pmid = {36939224}, issn = {1940-087X}, abstract = {The development and spread of antibiotic resistance (AR) through microbiota associated with freshwater bodies is a major global health concern. In the present study, freshwater samples were collected and analyzed with respect to the total bacterial diversity and AR genes (ARGs) using both conventional culture-based techniques and a high-throughput culture-independent metagenomic approach. This paper presents a systematic protocol for the enumeration of the total and antibiotic-resistant culturable bacteria from freshwater samples and the determination of phenotypic and genotypic resistance in the culturable isolates. Further, we report the use of whole metagenomic analysis of the total metagenomic DNA extracted from the freshwater sample for the identification of the overall bacterial diversity, including non-culturable bacteria, and the identification of the total pool of different ARGs (resistome) in the water body. Following these detailed protocols, we observed a high antibiotic-resistant bacteria load in the range of 9.6 × 10[5]-1.2 × 10[9] CFU/mL. Most isolates were resistant to the multiple tested antibiotics, including cefotaxime, ampicillin, levofloxacin, chloramphenicol, ceftriaxone, gentamicin, neomycin, trimethoprim, and ciprofloxacin, with multiple antibiotic resistance (MAR) indexes of ≥0.2, indicating high levels of resistance in the isolates. The 16S rRNA sequencing identified potential human pathogens, such as Klebsiella pneumoniae, and opportunistic bacteria, such as Comamonas spp., Micrococcus spp., Arthrobacter spp., and Aeromonas spp. The molecular characterization of the isolates showed the presence of various ARGs, such as blaTEM, blaCTX-M (β-lactams), aadA, aac (6')-Ib (aminoglycosides), and dfr1 (trimethoprims), which was also confirmed by the whole metagenomic DNA analysis. A high prevalence of other ARGs encoding for antibiotic efflux pumps-mtrA, macB, mdtA, acrD, β-lactamases-SMB-1, VIM-20, ccrA, ampC, blaZ, the chloramphenicol acetyltransferase gene catB10, and the rifampicin resistance gene rphB-was also detected in the metagenomic DNA. With the help of the protocols discussed in this study, we confirmed the presence of waterborne MAR bacteria with diverse AR phenotypic and genotypic traits. Thus, whole metagenomic DNA analysis can be used as a complementary technique to conventional culture-based techniques to determine the overall AR status of a water body.}, }
@article {pmid36939007, year = {2023}, author = {Yang, C and Lo, T and Nip, KM and Hafezqorani, S and Warren, RL and Birol, I}, title = {Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, doi = {10.1093/gigascience/giad013}, pmid = {36939007}, issn = {2047-217X}, support = {R01HG007182/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Nanopore sequencing is crucial to metagenomic studies as its kilobase-long reads can contribute to resolving genomic structural differences among microbes. However, sequencing platform-specific challenges, including high base-call error rate, nonuniform read lengths, and the presence of chimeric artifacts, necessitate specifically designed analytical algorithms. The use of simulated datasets with characteristics that are true to the sequencing platform under evaluation is a cost-effective way to assess the performance of bioinformatics tools with the ground truth in a controlled environment.<br><br>RESULTS: Here, we present Meta-NanoSim, a fast and versatile utility that characterizes and simulates the unique properties of nanopore metagenomic reads. It improves upon state-of-the-art methods on microbial abundance estimation through a base-level quantification algorithm. Meta-NanoSim can simulate complex microbial communities composed of both linear and circular genomes and can stream reference genomes from online servers directly. Simulated datasets showed high congruence with experimental data in terms of read length, error profiles, and abundance levels. We demonstrate that Meta-NanoSim simulated data can facilitate the development of metagenomic algorithms and guide experimental design through a metagenome assembly benchmarking task.<br><br>CONCLUSIONS: The Meta-NanoSim characterization module investigates read features, including chimeric information and abundance levels, while the simulation module simulates large and complex multisample microbial communities with different abundance profiles. All trained models and the software are freely accessible at GitHub: https://github.com/bcgsc/NanoSim.}, }
@article {pmid36938368, year = {2023}, author = {Sadasivan, H and Wadden, J and Goliya, K and Ranjan, P and Dickson, RP and Blaauw, D and Das, R and Narayanasamy, S}, title = {Rapid Real-time Squiggle Classification for Read until using RawMap.}, journal = {Archives of clinical and biomedical research}, volume = {7}, number = {1}, pages = {45-57}, pmid = {36938368}, issn = {2572-5017}, abstract = {ReadUntil enables Oxford Nanopore Technology's (ONT) sequencers to selectively sequence reads of target species in real-time. This enables efficient microbial enrichment for applications such as microbial abundance estimation and is particularly beneficial for metagenomic samples with a very high fraction of non-target reads (> 99% can be human reads). However, read-until requires a fast and accurate software filter that analyzes a short prefix of a read and determines if it belongs to a microbe of interest (target) or not. The baseline Read Until pipeline uses a deep neural network-based basecaller called Guppy and is slow and inaccurate for this task (~60% of bases sequenced are unclassified). We present RawMap, an efficient CPU-only microbial species-agnostic Read Until classifier for filtering non-target human reads in the squiggle space. RawMap uses a Support Vector Machine (SVM), which is trained to distinguish human from microbe using non-linear and non-stationary characteristics of ONT's squiggle output (continuous electrical signals). Compared to the baseline Read Until pipeline, RawMap is a 1327X faster classifier and significantly improves the sequencing time and cost, and compute time savings. We show that RawMap augmented pipelines reduce sequencing time and cost by ~24% and computing cost by 22%. Additionally, since RawMap is agnostic to microbial species, it can also classify microbial species it is not trained on. We also discuss how RawMap may be used as an alternative to the RT-PCR test for viral load quantification of SARS-CoV-2.}, }
@article {pmid36937305, year = {2023}, author = {Rocha, LO and Silva, NCC}, title = {Editorial: Application of omics-based technologies and the impact on food science.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1155757}, pmid = {36937305}, issn = {1664-302X}, }
@article {pmid36937300, year = {2023}, author = {Yoon, SJ and Yu, JS and Min, BH and Gupta, H and Won, SM and Park, HJ and Han, SH and Kim, BY and Kim, KH and Kim, BK and Joung, HC and Park, TS and Ham, YL and Lee, DY and Suk, KT}, title = {Bifidobacterium-derived short-chain fatty acids and indole compounds attenuate nonalcoholic fatty liver disease by modulating gut-liver axis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1129904}, pmid = {36937300}, issn = {1664-302X}, abstract = {Emerging evidences about gut-microbial modulation have been accumulated in the treatment of nonalcoholic fatty liver disease (NAFLD). We evaluated the effect of Bifidobacterium breve and Bifidobacterium longum on the NAFLD pathology and explore the molecular mechanisms based on multi-omics approaches. Human stool analysis [healthy subjects (n = 25) and NAFLD patients (n = 32)] was performed to select NAFLD-associated microbiota. Six-week-old male C57BL/6 J mice were fed a normal chow diet (NC), Western diet (WD), and WD with B. breve (BB) or B. longum (BL; 109 CFU/g) for 8 weeks. Liver/body weight ratio, histopathology, serum/tool analysis, 16S rRNA-sequencing, and metabolites were examined and compared. The BB and BL groups showed improved liver histology and function based on liver/body ratios (WD 7.07 ± 0.75, BB 5.27 ± 0.47, and BL 4.86 ± 0.57) and NAFLD activity scores (WD 5.00 ± 0.10, BB 1.89 ± 1.45, and BL 1.90 ± 0.99; p < 0.05). Strain treatment showed ameliorative effects on gut barrier function. Metagenomic analysis showed treatment-specific changes in taxonomic composition. The community was mainly characterized by the significantly higher composition of the Bacteroidetes phylum among the NC and probiotic-feeding groups. Similarly, the gut metabolome was modulated by probiotics treatment. In particular, short-chain fatty acids and tryptophan metabolites were reverted to normal levels by probiotics, whereas bile acids were partially normalized to those of the NC group. The analysis of gene expression related to lipid and glucose metabolism as well as the immune response indicated the coordinative regulation of β-oxidation, lipogenesis, and systemic inflammation by probiotic treatment. BB and BL attenuate NAFLD by improving microbiome-associated factors of the gut-liver axis.}, }
@article {pmid36937296, year = {2023}, author = {Tian, X and Li, D and Zhao, X and Xiao, Z and Sun, J and Yuan, T and Wang, Y and Zuo, X and Yang, G and Yu, T}, title = {Dietary grape pomace extract supplementation improved meat quality, antioxidant capacity, and immune performance in finishing pigs.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1116022}, pmid = {36937296}, issn = {1664-302X}, abstract = {In pig production, reducing production costs and improving immunity are important. Grape pomace, a good agricultural by-product, has been thrown away as food waste for a long time. Recently, we found that it could be used as a new source of pig feed. We investigated the effect of grape pomace on inflammation, gut barrier function, meat quality, and growth performance in finishing pigs. Our results indicated that treatment samples showed a significant decrease in water loss, IL-1β, DAO, ROS, and MDA content (p < 0.05). IgA, IgG, IgM, CAT, T-AOC, SOD, and IFN-γ significantly increased compared with those in control samples (p < 0.05). Meanwhile, the relative mRNA expression of the tight junction protein occludin showed a significant difference (p < 0.05). Analysis of metagenomic sequencing indicated that grape pomace significantly decreased the relative abundance of Treponema and Streptococcus (p < 0.05). In summary, our results demonstrated that grape pomace could improve meat quality, alleviate inflammation, and decrease oxidative stress.}, }
@article {pmid36937279, year = {2023}, author = {Kerr, EN and Papudeshi, B and Haggerty, M and Wild, N and Goodman, AZ and Lima, LFO and Hesse, RD and Skye, A and Mallawaarachchi, V and Johri, S and Parker, S and Dinsdale, EA}, title = {Stingray epidermal microbiomes are species-specific with local adaptations.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1031711}, pmid = {36937279}, issn = {1664-302X}, abstract = {Marine host-associated microbiomes are affected by a combination of species-specific (e.g., host ancestry, genotype) and habitat-specific features (e.g., environmental physiochemistry and microbial biogeography). The stingray epidermis provides a gradient of characteristics from high dermal denticles coverage with low mucus to reduce dermal denticles and high levels of mucus. Here we investigate the effects of host phylogeny and habitat by comparing the epidermal microbiomes of Myliobatis californica (bat rays) with a mucus rich epidermis, and Urobatis halleri (round rays) with a mucus reduced epidermis from two locations, Los Angeles and San Diego, California (a 150 km distance). We found that host microbiomes are species-specific and distinct from the water column, however composition of M. californica microbiomes showed more variability between individuals compared to U. halleri. The variability in the microbiome of M. californica caused the microbial taxa to be similar across locations, while U. halleri microbiomes were distinct across locations. Despite taxonomic differences, Shannon diversity is the same across the two locations in U. halleri microbiomes suggesting the taxonomic composition are locally adapted, but diversity is maintained by the host. Myliobatis californica and U. halleri microbiomes maintain functional similarity across Los Angeles and San Diego and each ray showed several unique functional genes. Myliobatis californica has a greater relative abundance of RNA Polymerase III-like genes in the microbiome than U. halleri, suggesting specific adaptations to a heavy mucus environment. Construction of Metagenome Assembled Genomes (MAGs) identified novel microbial species within Rhodobacteraceae, Moraxellaceae, Caulobacteraceae, Alcanivoracaceae and Gammaproteobacteria. All MAGs had a high abundance of active RNA processing genes, heavy metal, and antibiotic resistant genes, suggesting the stingray mucus supports high microbial growth rates, which may drive high levels of competition within the microbiomes increasing the antimicrobial properties of the microbes.}, }
@article {pmid36937148, year = {2023}, author = {Zheng, L and Kang, Z and Wang, R and Lv, M and Gao, Z and Xu, H and Wang, M}, title = {Evaluation of the Diagnostic Performance of mNGS in Detecting Intra-Abdominal Infections of the Emergency Department Patients.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {1421-1432}, pmid = {36937148}, issn = {1178-6973}, abstract = {PURPOSE: Intra-abdominal infections (IAI) are gradually becoming common in the emergency department, though the incidence is low and the prognosis is fair, as the symptoms are similar to other intra-abdominal diseases, rapid and accurate diagnosis of the causative agents is essential for clinical management. This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) in detecting IAI in the emergency department.<br><br>PATIENTS AND METHODS: This was a retrospective, single-centered study including patients admitted to the emergency department from January 1st, 2021 to August 31st, 2022 with diagnosis of IAI. The comparison between mNGS and microbial culture using paracentesis fluid samples was performed to evaluate the diagnostic performance of mNGS for IAI. Meanwhile, paracentesis fluid and peripheral blood mNGS were compared to explore the sample specificity. Further, the microbial community structure of the patients with pyogenic liver abscesses (PLA) was analyzed.<br><br>RESULTS: Thirty-four IAI patients including 23 with pyogenic liver abscesses (PLA), 3 with parapancreatic abscesses, and 8 with other IAI were included in this study. Compared with the conventional microbial culture of paracentesis fluid, mNGS using paracentesis fluid detected more positive cases of IAI (93.75% vs 81.25%), and identified more species of pathogens, especially in obligate anaerobes and viral pathogens. Peripheral blood mNGS presented a relatively high consistency with the paracentesis fluid mNGS (91% mutual positive). The microbial community structure of PLA patients with diabetes is less diverse than that of those without diabetes. Patients with diabetes are at high risk of PLA caused by Klebsiella pneumonia.<br><br>CONCLUSION: mNGS has advantages in detecting IAI in the emergency department, and peripheral blood mNGS can be a non-invasive choice for early diagnosis.}, }
@article {pmid36937145, year = {2023}, author = {Cheng, H and Tan, N and Lu, Y and Wu, H and Liu, Z and Zhang, D and Xu, Z and Li, C}, title = {Lumbar Spine Infection with Eikenella corrodens Presented as Abdominal Pain: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {1407-1417}, pmid = {36937145}, issn = {1178-6973}, abstract = {BACKGROUND: Eikenella corrodens is a part of the inherent flora on the surface of human mucosa. It usually does not cause disease unless the patient has been bitten, injured or surgically infected. Lumbar spine infection caused by Eikenella corrodens usually presents with conventional symptoms such as low back pain and fever. Herein, we report a case of lumbar intervertebral space infection with Eikenella corrodens presented as abdominal pain.<br><br>CASE PRESENTATION: A 38-year-old man with no medical history of note presented with abdominal pain. Initially, local doctors suspected that the patient had abdominal disease. However, abdominal diseases were ruled out and only lumbar spine infection was confirmed. Then, the patient was misdiagnosed as lumbar tuberculosis. Finally, anaerobic culture and metagenomic next-generation sequencing confirmed the Eikenella corrodens, which was rarely involved in lumbar intervertebral space infection. The patient recovered after operation and antibiotic therapy.<br><br>CONCLUSION: This case indicated a rare symptom of lumbar spine infection, abdominal cramping, which is caused by Eikenella corrodens. Blood culture had low sensitivity as a diagnostic method for Eikenella corrodens, but lesion sample culture or metagenomic next-generation sequencing had high sensitivity for early diagnosis.}, }
@article {pmid36937014, year = {2023}, author = {Zhang, L and Shen, H and Zhang, J and Mao, S}, title = {Variety of rumen microbial populations involved in biohydrogenation related to individual milk fat percentage of dairy cows.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1106834}, pmid = {36937014}, issn = {2297-1769}, abstract = {Our objective was to investigate the contribution of the rumen microbiome on the individual milk fat percentage (MFP) of Holstein dairy cows under the same nutritional and management conditions. From 92 early lactation dairy cows, the top 10 with the highest MFP (HF; n = 10) and the last 10 with the lowest MFP (LF; n = 10) were selected for the study. As a result, the milk trans-10, cis-12 C18:2 content was significant lower in the HF group than that in the LF group (P < 0.001). The rumen acetate to propionate ratio was significant higher in the HF group than that in the LF group (P = 0.035). According to the results of 16S rRNA gene sequencing, a minor but significant difference existed between the groups (P = 0.040). Three genera of the family Lachnospiraceae and four genera of the order Bacteroidales were identified to be the biomarkers for the LF group and HF group in the LEfSe analysis, respectively. Three microbial modules enriched by the family Lachnospiraceae were positively related to the milk trans-10, cis-12 C18:2 content (r s > 0.60, P < 0.05). According to the results of shotgun metagenome sequencing, three kinds of linoleic acid (LA) isomerase genes were present in the gene pools of the rumen microbiome. Among them, the relative abundance of Bifidobacterium LA isomerase (BBI) was higher in the HF group than that in the LF group (P = 0.007). Three metagenome-assembled genomes (MAGs) with LA isomerase genes were positively correlated to the milk trans-10, cis-12 C18:2 content (r s > 0.40, P < 0.05). Furthermore, all of these three MAGs were found to be able to produce lactate. Taken together, these results indicate that the increased relative abundance of microbial population with the trans-10 biohydrogenation pathway within the rumen microbiome contributes to the decrease of MFP via the increase of rumen trans-10, cis-12 C18:2 production. This study provides a new perspective for the development of measures for improving the milking performance of dairy cows.}, }
@article {pmid36936880, year = {2023}, author = {Morishima, S and Kawada, Y and Fukushima, Y and Takagi, T and Naito, Y and Inoue, R}, title = {A randomized, double-blinded study evaluating effect of matcha green tea on human fecal microbiota.}, journal = {Journal of clinical biochemistry and nutrition}, volume = {72}, number = {2}, pages = {165-170}, pmid = {36936880}, issn = {0912-0009}, abstract = {Matcha green tea is made from powdered green tea leaves. Unlike regular green tea, Matcha green tea is believed to exert beneficial effects on the gut microbiota, as it is richer in nutrients such as tea catechins and insoluble dietary fiber. In the present study, we aimed to investigate the effects of consumption of Matcha green tea on the gut microbiota. Human participants were randomly assigned to a placebo (n = 16) or a Matcha green tea (n = 17) drink group and asked to drink the treatments for two weeks. Feces were collected from the participants pre- and post-treatment and fecal microbiota composition was analyzed by 16S rRNA metagenomic sequencing. The beta-diversity of microbial composition significantly (p<0.05) changed in MGT group but not in placebo group. In addition, the number of unique bacterial genera significantly (p<0.05) changed in the Matcha green tea group was 30, while it was only 3 in the Placebo group. Increase and decrease in abundances of Coprococcus and Fusobacterium, respectively, in the gut microbiota of Matcha green tea group, conferred potential health benefits to the host. The present study was registered in the UMIN Clinical Trial Registry (UMIN000043857).}, }
@article {pmid36936777, year = {2023}, author = {Jia, K and Huang, S and Shen, C and Li, H and Zhang, Z and Wang, L and Zhao, G and Wu, Z and Lin, Y and Xia, H and Tang, M and Yang, H and Hu, H}, title = {Enhancing urinary tract infection diagnosis for negative culture patients with metagenomic next-generation sequencing (mNGS).}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1119020}, pmid = {36936777}, issn = {2235-2988}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a promising technology that allows unbiased pathogen detection and is increasingly being used for clinical diagnoses. However, its application in urinary tract infection (UTI) is still scarce.<br><br>METHODS: The medical records of 33 patients with suspected UTI who were admitted to the Second Hospital of Tianjin Medical University from March 2021 to July 2022 and received urine mNGS were retrospectively analyzed. The performance of mNGS and conventional urine culture in diagnosing infection and identifying causative organisms was compared, and the treatment effects were evaluated in terms of changes in urinalyses and urinary symptoms.<br><br>RESULTS: In the detection of bacteria and fungi, mNGS detected at least one pathogen in 29 (87.9%) cases, including 19 (57.6%) with positive mNGS but negative culture results and 10 (30.3%) with both mNGS and culture positive results. The remaining 4 (12.1%) patients were negative by both tests. Overall, mNGS performed better than culture (87.9% vs. 30.3%, P < 0.001). Within the 10 double-positive patients, mNGS matched culture results exactly in 5 cases, partially in 4 cases, and not at all in 1 case. In addition, mNGS detected a broader pathogen spectrum, detecting 26 species compared to only 5 species found in culture. The most abundant bacteria detected by mNGS was Escherichia coli, detected in 9 (27.2%) patients. All anaerobic bacteria, Mycobacterium Tuberculosis and all mixed pathogens were detected by mNGS. The final clinical diagnosis of UTI was made in 25 cases, and the sensitivity of mNGS was significantly higher than culture (100.0% vs 40.0%; P < 0.001) when using the diagnosis as a reference standard; the positive predictive value, negative predictive value and specificity were 86.2%, 100% and 50.0%, respectively. Importantly, targeted antibiotic therapy based on mNGS resulted in significant improvement in urinalyses and urinary symptoms in patients.<br><br>CONCLUSIONS: mNGS is a technology that has shown clear advantages over culture, particularly in the context of mixed infections and UTIs that are difficult to diagnose and treat. It helps to improve the detection of pathogens, guide changes in treatment strategies, and is an effective complement to urine culture.}, }
@article {pmid36936762, year = {2023}, author = {Cai, Y and Ding, H and Chen, X and Chen, Y and Huang, C and Zhang, C and Huang, Z and Huang, Y and Li, W and Zhang, W and Fang, X}, title = {Optimization and standardization of mNGS-based procedures for the diagnosis of Mycoplasma periprosthetic joint infection: A novel diagnostic strategy for rare bacterial periprosthetic joint infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1089919}, pmid = {36936762}, issn = {2235-2988}, abstract = {INTRODUCTION: The diagnosis of Mycoplasma periprosthetic joint infection (PJI) is rather difficult due to its rarity and difficult in isolation, there are not standardized diagnostic procedure for Mycoplasma PJI presently. This study aimed to reported a metagenomic next-generation sequencing (mNGS)-based diagnostic strategy for Mycoplasma PJI.<br><br>METHODS: In the present study, we have reported the largest number of Mycoplasma PJI that were precisely diagnosed by mNGS and verified by optimized microbial culture methods and (or) 16S PCR polymerase chain reaction (PCR).<br><br>RESULTS: The positive rate of optimized microbial culture methods and 16S PCR in the detection of Mycoplasma PJI was 57.14% and 71.43%, respectively. The infections were well controlled by targeted treatment in all cases.<br><br>CONCLUSION: The standardized and optimized procedure based on mNGS presented in this study is useful for the diagnosis of Mycoplasma PJI, which might also be provided as a novel diagnostic strategy for rare bacterial PJI.}, }
@article {pmid36936641, year = {2023}, author = {Taibukahn, N and Ab Majid, AH}, title = {Metagenomic 16S rDNA amplicon data of microbial diversity of Cimex hemipterus (F.) (Hemiptera: Cimicidae) treated with insect growth regulators (IGR).}, journal = {Data in brief}, volume = {47}, number = {}, pages = {109024}, pmid = {36936641}, issn = {2352-3409}, abstract = {The metagenomics dataset presented here is based on bacterial 16S rDNA gene amplicons of DNA extracted from tropical bed bugs (Cimex hemipterus). Amplicon-based sequencing was performed using the Illumina MiSeq platform, and the raw sequence data were analyzed using QIIME (version 2022.8.3). The metagenome sequence comprised ten samples that include C1 (133 511bps), C2 (108 920bps), CH1 (106 562bps), CH2 (101 778bps), P1 (103 618bps), P2 (133 258bps), T1 (113 558bps), T2 (133 952bps), TM1 (125 335bps), and TM2 (118 345bps). The sequence data is readily accessible at the NCBI SRA under bio project PRJNA918835. The most abundant microbial community present in the C. hemipterus is the Proteobacteria, with more than 99% of the abundance.}, }
@article {pmid36936223, year = {2023}, author = {Liao, Y and Xiao, J and Fang, F and Zhou, H and Liu, L and Liu, X}, title = {Case report: Acinetobacter baumannii septic arthritis in an immunocompetent infant.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1135178}, pmid = {36936223}, issn = {2296-858X}, abstract = {Acinetobacter baumannii is a gram-negative coccobacilli, mainly causing nosocomial infections with poor prognosis, especially in patients with prolonged hospitalization or antibiotics administration. A. baumannii pneumonia is the most common clinical form and usually occurs in critically ill patients in the intensive care unit. However, septic arthritis caused by A. baumannii is rarely reported. In this report, we describe a case of A. baumannii septic arthritis combined with incomplete Kawasaki disease in an infant. The child's chief complaint was a 2-week intermittent fever with poor response to antibiotics. Initial physical examination revealed swollen lymph nodes in the neck, pharynx congestion, and the appearance of rashes. Combined with laboratory tests, the diagnosis of incomplete Kawasaki disease was considered. After administration of high-dose intravenous immunoglobulin and corticosteroids, the child's fever improved and periungual desquamation appeared simultaneously. Swelling of the right knee occurred 5 days after the fever improved and imaging tests of MRI and ultrasound suggested the existence of infection. A diagnosis of septic arthritis was established subsequently, and arthroscopy was carried out. A. baumannii was finally identified by metagenomics next-generation sequencing of joint draining fluid for pathogenic microorganisms. Treatment with meropenem was then started. The patient eventually recovered and was discharged from the hospital after 23 days of treatment with meropenem. Although A. baumannii is not a common bacterium of septic arthritis, this rare infection can still occur in infants. Early diagnosis, pathogenic identification, and target antibiotic treatment are important to reduce the occurrence of joint sequelae.}, }
@article {pmid36935436, year = {2023}, author = {Kocak, FO and Tanir, SGE and Cetin, AK and Degirmenci, L}, title = {Correction: Simulatenous evaluation of composting experiments and metagenome analyses to illuminate the effect of Streptomyces spp. on organic matter degradation.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {39}, number = {5}, pages = {124}, doi = {10.1007/s11274-023-03523-5}, pmid = {36935436}, issn = {1573-0972}, }
@article {pmid36934910, year = {2023}, author = {Greses, S and De Bernardini, N and Treu, L and Campanaro, S and González-Fernández, C}, title = {Genome-centric metagenomics revealed the effect of pH on the microbiome involved in short-chain fatty acids and ethanol production.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {128920}, doi = {10.1016/j.biortech.2023.128920}, pmid = {36934910}, issn = {1873-2976}, abstract = {Added-value chemicals production via food waste (FWs) valorization using open-mixed cultures is an emerging approach to replace petrochemical-based compounds. Nevertheless, the effects of operational parameters on the product spectrum remain uncertain given the wide number of co-occurring species and metabolisms. In this study, the identification of 58 metagenome-assembled genomes and their investigation assessed the effect of slight pH variations on microbial dynamics and the corresponding functions when FWs were subjected to anaerobic fermentation (AF) in 1-L continuous stirred tank reactors at 25°C. The initial pH of 6.5 promoted a microbial community involved in acetate, butyrate and ethanol production, mediated by Bifidobacterium subtile IE007 and Eubacteriaceae IE027 as main species. A slight pH decrease to 6.1 shaped microbial functions that resulted in caproate and H2 production, increasing the relevance of Eubacteriaceae IE037 role. This study elucidated the strong pH effect on product outputs when minimal variations take place in AF.}, }
@article {pmid36934538, year = {2023}, author = {Dai, C and Qu, Y and Wu, W and Li, S and Chen, Z and Lian, S and Jing, J}, title = {QSP: An open sequence database for quorum sensing related gene analysis with an automatic annotation pipeline.}, journal = {Water research}, volume = {235}, number = {}, pages = {119814}, doi = {10.1016/j.watres.2023.119814}, pmid = {36934538}, issn = {1879-2448}, abstract = {Quorum sensing (QS) has attracted great attention due to its important role in the bacterial interactions and its relevance to water management. With the development of high-throughput sequencing technology, a specific database for QS-related sequence annotation is urgently needed. Here, Hidden Markov Model (HMM) profiles for 38 types of QS-related proteins were built using a total of 4024 collected seed sequences. Based on both homolog search and keywords confirmation against the non-redundant database, we established a QS-related protein (QSP) database, that includes 809,721 protein sequences and 186,133 nucleotide sequences, downloaded available at: https://github.com/chunxiao-dcx/QSP. The entries were classified into 38 types and 315 subtypes among 91 bacterial phyla. Furthermore, an automatic annotation pipeline, named QSAP, was developed for rapid annotation, classification and abundance quantification of QSP-like sequences from sequencing data. This pipeline provided the two homolog alignment strategies offered by Diamond (Blastp) or HMMER (Hmmscan), as well as a data cleansing function for a subset or union set of the hits. The pipeline was tested using 14 metagenomic samples from various water environments, including activated sludge, deep-sea sediments, estuary water, and reservoir water. The QSAP pipeline is freely available for academic use in the code repository at: https://github.com/chunxiao-dcx/QSAP. The establishment of this database and pipeline, provides a useful tool for QS-related sequence annotation in a wide range of projects, and will increase our understanding of QS communication in aquatic environments.}, }
@article {pmid36934439, year = {2023}, author = {Runde, J and Veseli, I and Fogarty, EC and Watson, AR and Clayssen, Q and Yosef, M and Shaiber, A and Verma, R and Quince, C and Gerasimidis, K and Rubin, DT and Eren, AM}, title = {Transient Suppression of Bacterial Populations Associated with Gut Health is Critical in Success of Exclusive Enteral Nutrition for Children with Crohn's Disease.}, journal = {Journal of Crohn's &amp; colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjad031}, pmid = {36934439}, issn = {1876-4479}, abstract = {BACKGROUND AND AIMS: Exclusive enteral nutrition [EEN] is a dietary intervention to induce clinical remission in children with active luminal Crohn's disease [CD]. While changes in the gut microbial communities have been implicated in achieving this remission, a precise understanding of the role of microbial ecology in the restoration of gut homeostasis is lacking.<br><br>METHODS: Here we reconstructed genomes from the gut metagenomes of 12 paediatric subjects who were sampled before, during and after EEN. We then classified each microbial population into distinct 'phenotypes' or patterns of response based on changes in their relative abundances throughout the therapy on a per-individual basis.<br><br>RESULTS: Our data show that children achieving clinical remission during therapy were enriched with microbial populations that were either suppressed or that demonstrated a transient bloom as a function of EEN. In contrast, this ecosystem-level response was not observed in cases of EEN failure. Further analysis revealed that populations that were suppressed during EEN were significantly more prevalent in healthy children and adults across the globe compared with those that bloomed ephemerally during the therapy.<br><br>CONCLUSIONS: These observations taken together suggest that successful outcomes of EEN are marked by a temporary emergence of microbial populations that are rare in healthy individuals, and a concomitant reduction in microbes that are commonly associated with gut homeostasis. Our work is a first attempt to highlight individual-specific, complex environmental factors that influence microbial response in EEN. This model offers a novel, alternative viewpoint to traditional taxonomic strategies used to characterize associations with health and disease states.}, }
@article {pmid36933736, year = {2023}, author = {Li, M and Wang, K and Zheng, W and Maddela, NR and Xiao, Y and Li, Z and Tawfik, A and Chen, Y and Zhou, Z}, title = {Metagenomics and network analysis decipher profiles and co-occurrence patterns of bacterial taxa in soils amended with biogas slurry.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {162911}, doi = {10.1016/j.scitotenv.2023.162911}, pmid = {36933736}, issn = {1879-1026}, abstract = {Microbial community and interaction play crucial roles in ecological functions of soil including nutrient cycling carbon storage, and water maintenance etc. Numerous studies have shown that the application of fertilizers alters bacterial diversity; However, it remains unknown whether and how the continuous application of biogas slurry from anaerobic digestion affects the spatiotemporal heterogeneity of soil layers, complexity and stability of microbial networks, and functions related to C and N cycling. Here, we investigated the bacterial taxa of purple soils treated with swine biogas slurry for four different periods (0, 1, 3 and 8 years) and five different soil depths (20, 40, 60, 80 and 100 cm). The results showed that the application period of biogas slurry and soil depth were two powerful drivers of bacterial diversity and communities. Biogas slurry input resulted in marked changes in the bacterial diversity and composition at the soil depths of 0-60 cm. The relative abundances of Acidobacteriota, Myxococcot, and Nitrospirota decreased, while Actinobacteria, Chloroflexi, and Gemmatimonadota increased with repeated biogas slurry input. The decreasing complexity and stability of the bacterial network with decreasing nodes, links, robustness, and cohesions were found with increasing years of biogas slurry application, suggesting that the bacterial network of soils treated by the biogas slurry became more vulnerability compared with the control. Also, the linkages between the keystone taxa and soil properties were weakened after biogas slurry input, leading to the cooccurrence patterns being less affected by the keystones in the high level of nutrients. Metagenomic analysis confirmed that biogas slurry input increased the relative abundance of liable-C degradation and denitrification genes, which could highly impact the network properties. Overall, our study could give comprehensive understandings on the impacts of biogas slurry amendment on soils, which could be useful for maintaining sustainable agriculture and soil health with liquid fertilization.}, }
@article {pmid36927601, year = {2023}, author = {Thorn, CS and Maness, RW and Hulke, JM and Delmore, KE and Criscione, CD}, title = {Population genomics of helminth parasites.}, journal = {Journal of helminthology}, volume = {97}, number = {}, pages = {e29}, doi = {10.1017/S0022149X23000123}, pmid = {36927601}, issn = {1475-2697}, mesh = {Humans ; Animals ; *Parasites/genetics ; Metagenomics ; *Helminths/genetics ; Genome ; Biodiversity ; }, abstract = {Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.}, }
@article {pmid36707341, year = {2023}, author = {Tibayrenc, M}, title = {Towards a general, worldwide, Plasmodium population genomics framework.}, journal = {Trends in parasitology}, volume = {39}, number = {4}, pages = {229-230}, doi = {10.1016/j.pt.2023.01.003}, pmid = {36707341}, issn = {1471-5007}, mesh = {*Metagenomics ; *Plasmodium/genetics ; Genomics ; Genome, Protozoan/genetics ; Plasmodium vivax ; }, }
@article {pmid36937228, year = {2017}, author = {Navas-Molina, JA and Hyde, ER and Sanders, J and Knight, R}, title = {The Microbiome and Big Data.}, journal = {Current opinion in systems biology}, volume = {4}, number = {}, pages = {92-96}, pmid = {36937228}, issn = {2452-3100}, abstract = {Microbiome datasets have expanded rapidly in recent years. Advances in DNA sequencing, as well as the rise of shotgun metagenomics and metabolomics, are producing datasets that exceed the ability of researchers to analyze them on their personal computers. Here we describe what Big Data is in the context of microbiome research, how this data can be transformed into knowledge about microbes and their functions in their environments, and how the knowledge can be applied to move microbiome research forward. In particular, the development of new high-resolution tools to assess strain-level variability (moving away from OTUs), the advent of cloud computing and centralized analysis resources such as Qiita (for sequences) and GNPS (for mass spectrometry), and better methods for curating and describing "metadata" (contextual information about the sequence or chemical information) are rapidly assisting the use of microbiome data in fields ranging from human health to environmental studies.}, }
@article {pmid36933668, year = {2023}, author = {Rohr, JC and Bourassa, KA and Thompson, DS and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Madan, A}, title = {History of childhood physical abuse is associated with gut microbiota diversity among adult psychiatric inpatients.}, journal = {Journal of affective disorders}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jad.2023.03.023}, pmid = {36933668}, issn = {1573-2517}, abstract = {BACKGROUND: Traumatic life events are associated with the development of psychiatric and chronic medical illnesses. This exploratory study examined the relationship between traumatic life events and the gut microbiota among adult psychiatric inpatients.<br><br>METHODS: 105 adult psychiatric inpatients provided clinical data and a single fecal sample shortly after admission. A modified version of the Stressful Life Events Screening Questionnaire was used to quantify history of traumatic life events. 16S rRNA gene sequencing was used to analyze the gut microbial community.<br><br>RESULTS: Gut microbiota diversity was not associated with overall trauma score or any of the three trauma factor scores. Upon item-level analysis, history of childhood physical abuse was uniquely associated with beta diversity. Linear Discriminant Analysis Effect Size (LefSe) analyses revealed that childhood physical abuse was associated with abundance of distinct bacterial taxa associated with inflammation.<br><br>LIMITATIONS: This study did not account for dietary differences, though diet was highly restricted as all participants were psychiatric inpatients. Absolute variance accounted for by the taxa was small though practically meaningful. The study was not powered for full subgroup analysis based on race and ethnicity.<br><br>CONCLUSIONS: This study is among the first to demonstrate a relationship between childhood physical abuse and gut microbiota composition among adult psychiatric patients. These findings suggest that early childhood adverse events may have long-conferred systemic consequences. Future efforts may target the gut microbiota for the prevention and/or treatment of psychiatric and medical risk associated with traumatic life events.}, }
@article {pmid36933314, year = {2023}, author = {Su, C and Xian, Y and Qin, R and Zhou, Y and Lu, M and Wan, X and Chen, Z and Chen, M}, title = {Fe(III) enhances Cr(VI) bioreduction in a MFC-granular sludge coupling system: Experimental evidence and metagenomics analysis.}, journal = {Water research}, volume = {235}, number = {}, pages = {119863}, doi = {10.1016/j.watres.2023.119863}, pmid = {36933314}, issn = {1879-2448}, abstract = {The influence of Fe(III) on the bioreduction efficiency of Cr(VI) in a microbial fuel cell (MFC)-granular sludge coupling system using dissolved methane as an electron donor and carbon source was explored, and the mechanism of Fe(III) mediating enhancement in the bioreduction process of Cr(VI) in the coupling system was also investigated. Results showed that the presence of Fe(III) enhanced the ability of the coupling system to reduce Cr(VI). The average removal efficiencies of Cr(VI) in the anaerobic zone in response to 0, 5, and 20 mg/L of Fe(III) were 16.53±2.12%, 24.17±2.10%, and 46.33±4.41%, respectively. Fe(III) improved the reducing ability and output power of the system. In addition, Fe(III) enhanced the electron transport systems activity of the sludge, the polysaccharide and protein content in the anaerobic sludge. Meanwhile, X-ray photoelectron spectrometer (XPS) spectra demonstrated that Cr(VI) was reduced to Cr(III), while Fe2p participated in reducing Cr(VI) in the form of Fe(III) and Fe(II). Proteobacteria, Chloroflexi, and Bacteroidetes were the dominant phylum in the Fe(III)-enhanced MFC-granular sludge coupling system, accounting for 49.7%-81.83% of the microbial community. The relative abundance of Syntrophobacter and Geobacter increased after adding Fe(III), indicating that Fe(III) contributed to the microbial mediated anaerobic oxidation of methane (AOM) and bioreduction of Cr(VI). The genes mcr, hdr, and mtr were highly expressed in the coupling system after the Fe(III) concentration increased. Meanwhile, the relative abundances of coo and aacs genes were up-regulated by 0.014% and 0.075%, respectively. Overall, these findings deepen understanding of the mechanism of the Cr(VI) bioreduction in the MFC-granular sludge coupling system driven by methane under the influence of Fe(III).}, }
@article {pmid36933182, year = {2023}, author = {Li, J and Huang, T and Zhang, M and Tong, X and Chen, J and Zhang, Z and Huang, F and Ai, H and Huang, L}, title = {Metagenomic sequencing reveals swine lung microbial communities and metagenome-assembled genomes associated with lung lesions-a pilot study.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {36933182}, issn = {1618-1905}, abstract = {Low microbial biomass in the lungs, high host-DNA contamination and sampling difficulty limit the study on lung microbiome. Therefore, little is still known about lung microbial communities and their functions. Here, we perform a preliminary exploratory study to investigate the composition of swine lung microbial community using shotgun metagenomic sequencing and compare the microbial communities between healthy and severe-lesion lungs. We collected ten lavage-fluid samples from swine lungs (five from healthy lungs and five from severe-lesion lungs), and obtained their metagenomes by shotgun metagenomic sequencing. After filtering host genomic DNA contamination (93.5% ± 1.2%) in the lung metagenomic data, we annotated swine lung microbial communities ranging from four domains to 645 species. Compared with previous taxonomic annotation of the same samples by the 16S rRNA gene amplicon sequencing, it annotated the same number of family taxa but more genera and species. We next performed an association analysis between lung microbiome and host lung-lesion phenotype. We found three species (Mycoplasma hyopneumoniae, Ureaplasma diversum, and Mycoplasma hyorhinis) were associated with lung lesions, suggesting they might be the key species causing swine lung lesions. Furthermore, we successfully reconstructed the metagenome-assembled genomes (MAGs) of these three species using metagenomic binning. This pilot study showed us the feasibility and relevant limitations of shotgun metagenomic sequencing for the characterization of swine lung microbiome using lung lavage-fluid samples. The findings provided an enhanced understanding of the swine lung microbiome and its role in maintaining lung health and/or causing lung lesions.}, }
@article {pmid36933058, year = {2023}, author = {Balachandran, KRS and Sankara Subramanianan, SH and Dhassiah, MP and Rengarajan, A and Chandrasekaran, M and Rangamaran, VR and Gopal, D}, title = {Microbial community structure and exploration of bioremediation enzymes: functional metagenomics insight into Arabian Sea sediments.}, journal = {Molecular genetics and genomics : MGG}, volume = {}, number = {}, pages = {}, pmid = {36933058}, issn = {1617-4623}, abstract = {Deep-sea sediments provide important information on oceanic biogeochemical processes mediated by the microbiome and their functional roles which could be unravelled using genomic tools. The present study aimed to delineate microbial taxonomic and functional profiles from Arabian Sea sediment samples through whole metagenome sequencing using Nanopore technology. Arabian Sea is considered as a major microbial reservoir with significant bio-prospecting potential which needs to be explored extensively using recent advances in genomics. Assembly, co-assembly, and binning methods were used to predict Metagenome Assembled Genomes (MAGs) which were further characterized by their completeness and heterogeneity. Nanopore sequencing of Arabian Sea sediment samples generated around 1.73 tera basepairs of data. Proteobacteria (78.32%) was found to be the most dominant phylum followed by Bacteroidetes (9.55%) and Actinobacteria (2.14%) in the sediment metagenome. Further, 35 MAGs from assembled and 38 MAGs of co-assembled reads were generated from long-read sequence dataset with major representations from the genera Marinobacter, Kangiella, and Porticoccus. RemeDB analysis revealed a high representation of pollutant-degrading enzymes involved in hydrocarbon, plastic and dye degradation. Validation of enzymes with long nanopore reads using BlastX resulted in better characterization of complete gene signatures involved in hydrocarbon (6-monooxygenase and 4-hydroxyacetophenone monooxygenase) and dye degradation (Arylsulfatase). Enhancing the cultivability of deep-sea microbes predicted from the uncultured WGS approaches by I-tip method resulted in isolation of facultative extremophiles. This study presents a comprehensive insight into the taxonomic and functional profiles of Arabian Sea sediments, indicating a potential hotspot for bioprospection.}, }
@article {pmid36932631, year = {2023}, author = {Wen, T and Ding, Z and Thomashow, LS and Hale, L and Yang, S and Xie, P and Liu, X and Wang, H and Shen, Q and Yuan, J}, title = {Deciphering the mechanism of fungal pathogen-induced disease-suppressive soil.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18886}, pmid = {36932631}, issn = {1469-8137}, abstract = {One model of a disease-suppressive soil predicts that the confrontation of plant with a phytopathogen can lead to the recruitment and accumulation of beneficial microorganisms. However, more information is need to be deciphered regarding which beneficial microbes become enriched, and how the disease suppression is achieved. Here, we conditioned soil by continuously growing eight generations of cucumber inoculated with Fusarium oxysporum f.sp. cucumerinum in a split-root- system. Disease incidence was found to decrease gradually upon pathogen infection accompanied with higher quantity of reactive oxygen species (ROS mainly OH·) in roots and accumulation of Bacillus and Sphingomonas. These key microbes were proven to protect the cucumber from pathogen infection by inducing high ROS level in the roots through enrichment of pathways, including a two-component system, a bacterial secretion system and flagellar assembly revealed by metagenomics sequencing. Untargeted metabolomics analysis combined with in vitro application assays suggested that threonic acid and lysine were pivotal to recruit Bacillus and Sphingomonas. Collectively, our study deciphered a "cry for help" case wherein cucumber releases particular compounds to enrich beneficial microbes that raise the ROS level of host to prevent pathogen attack. More importantly, this may be one of the fundamental mechanisms underpinning disease-suppressive soil formation.}, }
@article {pmid36931530, year = {2023}, author = {Li, J and Zhu, S and Wang, Y and Fan, M and Dai, J and Zhu, C and Xu, K and Cui, M and Suo, C and Jin, L and Jiang, Y and Chen, X}, title = {Metagenomic association analysis of cognitive impairment in community-dwelling older adults.}, journal = {Neurobiology of disease}, volume = {}, number = {}, pages = {106081}, doi = {10.1016/j.nbd.2023.106081}, pmid = {36931530}, issn = {1095-953X}, abstract = {The gut microbiota is reportedly involved in neurodegenerative disorders, and exploration of differences in the gut microbiota in different cognitive status could provide clues for early detection and intervention in cognitive impairment. Here, we used data from the Taizhou Imaging Study (N = 516), a community-based cohort, to compare the overall structure of the gut microbiota at the species level through metagenomic sequencing, and to explore associations with cognition. Interestingly, bacteria capable of producing short-chain fatty acids (SCFAs), such as Bacteroides massiliensis, Bifidobacterium pseudocatenulatum, Fusicatenibacter saccharivorans and Eggerthella lenta, that can biotransform polyphenols, were positively associated with better cognitive performance (p < 0.05). Although Diallister invisus and Streptococcus gordonii were not obviously related to cognition, the former was dominant in individuals with mild cognitive impairment (MCI), while the later was more abundant in cognitively normal (CN) than MCI groups, and positively associated with cognitive performance (p < 0.05). Functional analysis further supported a potential role of SCFAs and lactic acid in the association between the gut microbiota and cognition. The significant associations persisted after accounting for dietary patterns. Collectively, our results demonstrate an association between the gut microbiota and cognition in the general population, indicating a potential role in cognitive impairment. The findings provide clues for microbiome biomarkers of dementia, and insight for the prevention and treatment of dementia.}, }
@article {pmid36931448, year = {2023}, author = {Li, W and Pang, L and Chatzisymeon, E and Yang, P}, title = {Effects of micron-scale zero valent iron on behaviors of antibiotic resistance genes and pathogens in thermophilic anaerobic digestion of waste activated sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {128895}, doi = {10.1016/j.biortech.2023.128895}, pmid = {36931448}, issn = {1873-2976}, abstract = {This work investigated the metagenomics-based behavior and risk of antibiotic resistance genes (ARGs), and their potential hosts during thermophilic anaerobic digestion (TAD) of waste activated sludge, enhanced by micron-scale zero valent iron (mZVI). Tests were conducted with 0, 25, 100, and 250 mg mZVI/g total solids (TS). Results showed that up to 7.3% and 4.8% decrease in ARGs' abundance and diversity, respectively, were achieved with 100 mg mZVI/g TS. At these conditions, ARGs with health risk in abundance and human pathogenic bacteria (HPB) diversity were also decreased by 8.3% and 3.6%, respectively. Additionally, mZVI reduced abundance of 72 potential pathogenic supercarriers for ARGs with high health risk by 2.5%, 5.0%, and 6.1%, as its dosage increased. Overall, mZVI, especially at 100 mg/g TS, can mitigate antibiotic resistance risk in TAD. These findings are important for better understanding risks of ARGs and their pathogenic hosts in ZVI-enhanced TAD of solid wastes.}, }
@article {pmid36931374, year = {2023}, author = {Yan, F and Wang, S and Huang, Z and Liu, Y and He, L and Qian, F}, title = {Microbial ecological responses of partial nitritation/anammox granular sludge to real water matrices and its potential application.}, journal = {Environmental research}, volume = {226}, number = {}, pages = {115701}, doi = {10.1016/j.envres.2023.115701}, pmid = {36931374}, issn = {1096-0953}, abstract = {Granular sludges are commonly microbial aggregates used to apply partial nitritation/anammox (PN/A) processes during efficient biological nitrogen removal from ammonium-rich wastewater. Considering keystone taxa of anammox bacteria (AnAOB) in granules and their sensitivity to unfavorable environments, it is essential to investigate microbial responses of autotrophic PN/A granules to real water matrices containing organic and inorganic pollutants. In this study, tap water, surface water, and biotreated wastewater effluents were fed into a series of continuous PN/A granular reactors, respectively, and the differentiation in functional activity, sludge morphology, microbial community structure, and nitrogen metabolic pathways was analyzed by integrating kinetic batch testing, size characterization, and metagenomic sequencing. The results showed that feeding of biotreated wastewater effluents causes significant decreases in nitrogen removal activity and washout of AnAOB (dominated by Candidatus Kuenenia) from autotrophic PN/A granules due to the accumulation of heavy metals and formation of cavities. Microbial co-occurrence networks and nitrogen cycle-related genes provided evidence for the high dependence of symbiotic heterotrophs (such as Proteobacteria, Chloroflexi, and Bacteroidetes) on anammox metabolism. The enhancement of Nitrosomonas nitritation in the granules would be considered as an important contributor to greenhouse gas (N2O) emissions from real water matrices. In a novel view on the application of microbial responses, we suggest a bioassay of PN/A granules by size characterization of red-color cores in ecological risk assessment of water environments.}, }
@article {pmid36931186, year = {2023}, author = {Yang, Y and Deng, Y and Shi, X and Liu, L and Yin, X and Zhao, W and Li, S and Yang, C and Zhang, T}, title = {QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification.}, journal = {Water research}, volume = {235}, number = {}, pages = {119858}, doi = {10.1016/j.watres.2023.119858}, pmid = {36931186}, issn = {1879-2448}, abstract = {The majority of the current regulatory practices for routine monitoring of beach water quality rely on the culture-based enumeration of faecal indicator bacteria (FIB) to develop criteria for promoting the general public's health. To address the limitations of culture methods and the arguable reliability of FIB in indicating health risks, we developed a Nanopore metagenomic sequencing-based viable cell absolute quantification workflow to rapidly and accurately estimate a broad range of microbes in beach waters by a combination of propidium monoazide (PMA) and cellular spike-ins. Using the simple synthetic bacterial communities mixed with viable and heat-killed cells, we observed near-complete relic DNA removal by PMA with minimal disturbance to the composition of viable cells, demonstrating the feasibility of PMA treatment in profiling viable cells by Nanopore sequencing. On a simple mock community comprised of 15 prokaryotic species, our results showed high accordance between the expected and estimated concentrations, suggesting the accuracy of our method in absolute quantification. We then further assessed the accuracy of our method for counting viable Escherichia coli and Vibrio spp. in beach waters by comparing to culture-based method, which were also in high agreement. Furthermore, we demonstrated that 1 Gb sequences obtained within 2 h would be sufficient to quantify a species having a concentration of ≥ 10 cells/mL in beach waters. Using our viability-resolved quantification workflow to assess the microbial risk of the beach water, we conducted (1) screening-level quantitative microbial risk assessment (QMRA) to investigate human illness risk and site-specific risk patterns that might guide risk management efforts and (2) metagenomics-based resistome risk assessment to evaluate another layer of risk caused by difficult illness treatment due to antimicrobial resistance (AMR). In summary, our metagenomic workflow for the rapid absolute quantification of viable bacteria demonstrated its great potential in paving new avenues toward holistic microbial risk assessment.}, }
@article {pmid36931127, year = {2023}, author = {Kugarajah, V and Nisha, KN and Jayakumar, R and Sahabudeen, S and Ramakrishnan, P and Mohamed, SB}, title = {Significance of microbial genome in environmental remediation.}, journal = {Microbiological research}, volume = {271}, number = {}, pages = {127360}, doi = {10.1016/j.micres.2023.127360}, pmid = {36931127}, issn = {1618-0623}, abstract = {Environmental pollutants seriously threaten the ecosystem and health of various life forms, particularly with the rapid industrialization and emerging population. Conventionally physical and chemical strategies are being opted for the removal of these pollutants. Bioremediation, through several advancements, has been a boon to combat the existing threat faced today. Microbes with enzymes degrade various pollutants and utilize them as a carbon and energy source. With the existing demand and through several research explorations, Genetically Engineered Microorganisms (GEMs) have paved to be a successful approach to abate pollution through bioremediation. The genome of the microbe determines its biodegradative nature. Thus, methods including pure culture techniques and metagenomics are used for analyzing the genome of microbes, which provides information about catabolic genes. The information obtained along with the aid of biotechnology helps to construct GEMs that are cost-effective and safer thereby exhibiting higher degradation of pollutants. The present review focuses on the role of microbes in the degradation of environmental pollutants, role of evolution in habitat and adaptation of microbes, microbial degenerative genes, their pathways, and the efficacy of recombinant DNA (rDNA) technology for creating GEMs for bioremediation. The present review also provides a gist of existing GEMs for bioremediation and their limitations, thereby providing a future scope of implementation of these GEMs for a sustainable environment.}, }
@article {pmid36931094, year = {2023}, author = {Correia, GD and Marchesi, JR and MacIntyre, DA}, title = {Moving beyond DNA: towards functional analysis of the vaginal microbiome by non-sequencing-based methods.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102292}, doi = {10.1016/j.mib.2023.102292}, pmid = {36931094}, issn = {1879-0364}, abstract = {Over the last two decades, sequencing-based methods have revolutionised our understanding of niche-specific microbial complexity. In the lower female reproductive tract, these approaches have enabled identification of bacterial compositional structures associated with health and disease. Application of metagenomics and metatranscriptomics strategies have provided insight into the putative function of these communities but it is increasingly clear that direct measures of microbial and host cell function are required to understand the contribution of microbe-host interactions to pathophysiology. Here we explore and discuss current methods and approaches, many of which rely upon mass-spectrometry, being used to capture functional insight into the vaginal mucosal interface. In addition to improving mechanistic understanding, these methods offer innovative solutions for the development of diagnostic and therapeutic strategies designed to improve women's health.}, }
@article {pmid36930418, year = {2023}, author = {Thakur, N and Nigam, M and Awasthi, G and Shukla, A and Shah, AA and Negi, N and Khan, SA and Casini, R and Elansary, HO}, title = {Synergistic soil-less medium for enhanced yield of crops: a step towards incorporating genomic tools for attaining net zero hunger.}, journal = {Functional &amp; integrative genomics}, volume = {23}, number = {2}, pages = {86}, pmid = {36930418}, issn = {1438-7948}, abstract = {Globally, industrial farming endangers crucial ecological mechanisms upon which food production relies, while 815 million people are undernourished and a significant number are malnourished. Zero Hunger aims to concurrently solve global ecological sustainability and food security concerns. Recent breakthroughs in molecular tools and approaches have allowed scientists to detect and comprehend the nature and structure of agro-biodiversity at the molecular and genetic levels, providing us an advantage over traditional methods of crop breeding. These bioinformatics techniques let us optimize our target plants for our soil-less medium and vice versa. Most of the soil-borne and seed-borne diseases are the outcomes of non-treated seed and growth media, which are important factors in low productivity. The farmers do not consider these issues, thereby facing problems growing healthy crops and suffering economic losses. This study is going to help the farmers increase their eco-friendly, chemical residue-free, quality yield of crops and their economic returns. The present invention discloses a synergistic soil-less medium that consists of only four ingredients mixed in optimal ratios by weight: vermicompost (70-80%), vermiculite (10-15%), coco peat (10-15%), and Rhizobium (0-1%). The medium exhibits better physical and chemical characteristics than existing conventional media. The vermiculite to coco peat ratio is reduced, while the vermicompost ratio is increased, with the goals of lowering toxicity, increasing plant and water holding capacity, avoiding drying of the media, and conserving water. The medium provides balanced nutrition and proper ventilation for seed germination and the growth of seedlings. Rhizobium is also used to treat the plastic bags and seeds. The results clearly show that the current synergistic soil-less environment is best for complete plant growth. Securing genetic advantages via sexual recombination, induced random mutations, and transgenic techniques have been essential for the development of improved agricultural varieties. The recent availability of targeted genome-editing technology provides a new path for integrating beneficial genetic modifications into the most significant agricultural species on the planet. Clustered regularly interspaced short palindromic repeats and associated protein 9 (CRISPR/Cas9) has evolved into a potent genome-editing tool for imparting genetic modifications to crop species. In addition, the integration of analytical methods like population genomics, phylogenomics, and metagenomics addresses conservation problems, while whole genome sequencing has opened up a new dimension for explaining the genome architecture and its interactions with other species. The in silico genomic and proteomic investigation was also conducted to forecast future investigations for the growth of French beans on a synergistic soil-less medium with the purpose of studying how a blend of vermicompost, vermiculite, cocopeat, and Rhizobium secrete metal ions, and other chemical compounds into the soil-less medium and affect the development of our target plant as well as several other plants. This interaction was studied using functional and conserved region analysis, phylogenetic analysis, and docking tools.}, }
@article {pmid36930078, year = {2023}, author = {Zhang, J and Xu, G and Shen, J and Ye, G}, title = {Pulmonary infection of Schizophyllum commune diagnosed by metagenomic next- generation sequencing: A case report.}, journal = {Medicine}, volume = {102}, number = {11}, pages = {e31465}, doi = {10.1097/MD.0000000000031465}, pmid = {36930078}, issn = {1536-5964}, abstract = {RATIONALE: Fungal infection is common and difficult to be diagnosed timely in clinical, for its various kinds and similar manifestations. The rare pulmonary fungal infection such as Schizophyllum commune was one of the harder ones and misdiagnosed in usual.<br><br>PATIENT CONCERNS: We report a 32-year-old female which was diagnosed with Metagenomic Next-Generation Sequencing (mNGS). She was hospitalized with the complaint of 4 months and more of repeated cough and expectorating. The chest computer tomography revealed left lower lobe pathological changes, but antibiotics were ineffective. No positive results were found in laboratory tests, including sputum culture and the pathology of lung puncture biopsy.<br><br>DIAGNOSES: mNGS of lung biopsy was performed and detected the sequence number of Schizophyllum for 11.<br><br>INTERVENTIONS: The patient was treated with voriconazole and itraconazole successively.<br><br>OUTCOMES: She recovered to health. There was no recurrence during follow-up.<br><br>LESSONS: mNGS as a diagnostic method could quickly detect pathogens through the processing of fragment, synthesis, comparison, and analysis of sample genes. It is suitable for detecting especially rare and polymicrobial infections. To our best knowledge, infection of Schizophyllum commune have not been reported in English literature with diagnostic method of mNGS.}, }
@article {pmid36929690, year = {2023}, author = {Zhu, N and Zhou, D and Yuan, R and Ruzetuoheti, Y and Li, J and Zhang, X and Li, S}, title = {Identification and comparison of Chlamydia psittaci, Legionella and Mycoplasma pneumonia infection.}, journal = {The clinical respiratory journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/crj.13603}, pmid = {36929690}, issn = {1752-699X}, abstract = {INTRODUCTION: Conventional etiological detection and pathogenic antibody methods make it challenging to identify the atypical pathogens among the community-acquired pneumonia (CAP). Metagenomic next-generation sequencing (mNGS) could rapidly detect all potentially infectious diseases and identifies novel or potential pathogens.<br><br>METHODS: Eighteen patients diagnosed with atypical CAP were enrolled in this retrospective study, including nine Chlamydia psittaci pneumonia (C. p), four Legionella pneumonia (L. p) and five Mycoplasma pneumonia (M. p). We simultaneously tested bronchoalveolar lavage fluid (BALF) samples for conventional microbiological methods and mNGS, and blood specimens were analysed. We also collected and compared baseline and clinical characteristics and treatment responses.<br><br>RESULTS: Patients with C. p and L. p had similar symptoms, including fever, cough, headache, dyspnoea, asthenia, shivering and headache, compared with M. p, whose symptoms were slight. C. p and L. p usually showed multiple lobar distributions with pleural effusion. Serologic testing indicated that L. p had higher levels of white blood cells (WBCs), neutrophils, C-reactive protein (CRP), procalcitonin (PCT), alanine aminotransferase (ALT), lactate dehydrogenase (LDH) and creatinine compared with M. p and L. p (p&#x2009;<&#x2009;0.05). However, patients with C. p had lower levels of albumin (p&#x2009;<&#x2009;0.05), and M. p had a minimum risk of cardiac volume loads (p&#x2009;<&#x2009;0.05). CD4/CD8 ratio, lymphocytes, aspartate aminotransferase (AST), creatine kinase (CK), cell counting of BALF and coagulation had no difference (p&#x2009;<&#x2009;0.05). Pathogenic IgM assay showed that 4/5 cases were positive for M. p and no positive detection for C. p and L. p infection. We timely adjusted the antibiotics according to the final mNGS results. Eventually, 16/18 patients recovered fully. Conditions of L. p patients were worse than those of C. p patients, and those of M. p patients were the least.<br><br>CONCLUSION: Early application of mNGS detection increased the atypical pathogenic identification, improved the prognosis and made up for the deficiency of conventional detection methods.}, }
@article {pmid36929191, year = {2023}, author = {Sharma, P and Singh, S and Das, K and Mahant, S and Das, R}, title = {Dysbiosis of gut microbiota due to diet, alcohol intake, body mass index, and gastrointestinal diseases in India.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {36929191}, issn = {1432-0614}, abstract = {The human gut is composed of diverse microflora which is influenced by dietary intake. Body mass index (BMI) and lifestyle patterns also play a vital role in human health to alter gut microbial composition. Our study aims to determine the impact of alcohol intake, BMI, and diet on gut microbiota and its relationship with gastrointestinal disorders. Thirty-nine gastric biopsies were taken from patients with various gastrointestinal (GI) diseases, and all the patient's lifestyle behavior were recorded in a written proforma. 16S rRNA metagenome analysis for V3-V4 regions was used to examine microbial compositions. The richness and diversity of gut microbiota were analyzed by PERMANOVA using the Bray-Curtis dissimilarity index and principal component analysis. The difference in relative abundance was calculated by ANOVA (p < 0.05). Alpha diversity indexes between vegetarians and non-vegetarians showed no significant difference based on BMI, alcohol status, and GI diseases. We found that in overweight vegetarian individuals Faecalibacterium and Rumicococcus might play a role in the control of Helicobacter pylori. Similarly, the increased abundance of Akkermansia muciniphila in non-vegetarian individuals with normal BMI might play a role to decrease the level of harmful bacteria like H. pylori, and Corynebacterium sp. Also, the relative abundance of Corynebacterium sp. among the vegetarians and Streptococcus sp. in the non-vegetarians was increased in alcoholics while H. pylori was increased in non-alcoholics irrespective of diet. There is an increased abundance of Faecalibacterium prausnitzii in vegetarians among all categories; however, we did not find any correlation between disease outcomes. Our study shows that alcohol intake and dietary habits have independent effects on gut microbial composition. The relative abundance of F. prausnitzii was high among vegetarians in all categories. KEY POINTS: • The presence of H. pylori is less among alcoholics. • Good bacteria help to maintain a normal body mass index. • Gut microbiota richness is high in vegetarians and diversity in non-vegetarians.}, }
@article {pmid36929080, year = {2023}, author = {Ma, S and Li, H}, title = {Statistical and Computational Methods for Microbial Strain Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2629}, number = {}, pages = {231-245}, pmid = {36929080}, issn = {1940-6029}, abstract = {Microbial strains are interpreted as a lineage derived from a recent ancestor that have not experienced "too many" recombination events and can be successfully retrieved with culture-independent techniques using metagenomic sequencing. Such a strain variability has been increasingly shown to display additional phenotypic heterogeneities that affect host health, such as virulence, transmissibility, and antibiotics resistance. New statistical and computational methods have recently been developed to track the strains in samples based on shotgun metagenomics data either based on reference genome sequences or Metagenome-assembled genomes (MAGs). In this paper, we review some recent statistical methods for strain identifications based on frequency counts at a set of single nucleotide variants (SNVs) within a set of single-copy marker genes. These methods differ in terms of whether reference genome sequences are needed, how SNVs are called, what methods of deconvolution are used and whether the methods can be applied to multiple samples. We conclude our review with areas that require further research.}, }
@article {pmid36929079, year = {2023}, author = {Kim, Y}, title = {Bioinformatic and Statistical Analysis of Microbiome Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2629}, number = {}, pages = {183-229}, pmid = {36929079}, issn = {1940-6029}, abstract = {Since advances in next-generation sequencing (NGS) technique enabled to investigate uncultured microbiota and their genomes in unbiased manner, many microbiome researches have been reporting strong evidences for close links of microbiome to human health and disease. Bioinformatic and statistical analysis of NGS-based microbiome data are essential components in those microbiome researches to explore the complex composition of microbial community and understand the functions of community members in relation to host and environment. This chapter introduces bioinformatic analysis methods that generate taxonomy and functional feature count table along with phylogenetic tree from raw NGS microbiome data and then introduce statistical methods and machine learning approaches for analyzing the outputs of the bioinformatic analysis to infer the biodiversity of a microbial community and unravel host-microbiome association. Understanding the advantages and limitations of the analysis methods will help readers use the methods correctly in microbiome data analysis and may give a new opportunity to develop new analytic techniques for microbiome research.}, }
@article {pmid36928747, year = {2023}, author = {Zhang, Y and Liu, F and Liang, H and Gao, D}, title = {Correction to: Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline Alkaline Wetland: a Metagenomic Analysis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-023-02205-x}, pmid = {36928747}, issn = {1432-184X}, }
@article {pmid36928716, year = {2023}, author = {Wahlen, BD and Wendt, LM and St Germain, CC and Traynor, SM and Barboza, C and Dempster, T and Gerken, H and McGowen, J and You, Y}, title = {Effect of nitrogen management in cultivation on the stability and microbial community of post-harvest Monoraphidium sp. algae biomass.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jimb/kuad004}, pmid = {36928716}, issn = {1476-5535}, abstract = {Seasonal variation in algae biomass productivity is a significant obstacle to the economical production of fuels and chemicals from algae biomass. Long-term storage is necessary to guarantee a constant supply to a conversion facility and harvested microalgae biomass (20% solids) is subject to degradation immediately upon harvesting as a result of aerobic instability. Ensiling has been successfully used to preserve microalgal biomass, but biomass attributes that contribute to successful storage are poorly understood. Storage studies of Monoraphidium sp. biomass indicate a strong correlation between nitrogen management in algae cultivation and stability of post-harvest algae biomass in 30 days of anaerobic storage. Algae cultivated with periodic nitrogen addition stored poorly (> 20% loss, dry basis), while algae biomass from cultures that were allowed to continue growing after nitrogen depletion was more stable in storage (8% loss, dry basis). A follow-up study aimed at exploring the relationship between nitrogen management in cultivation and stability of post-harvest algae biomass stored Monoraphidium biomass cultivated in nitrogen deplete and nitrogen replete conditions, as well as with blends of each in varying ratios. Monoraphidium biomass from nitrogen replete cultivations experienced the largest degradation (24%, dry basis), while nitrogen deplete biomass experienced the least (10%, dry basis). Dry matter loss experienced during storage of blends was positively correlated with the amount of nitrogen replete biomass that a blend contained. The composition of the post-storage algae microbial community was also strongly affected by cultivation conditions, with Clostridia species being more prevalent in stored biomass obtained from nitrogen replete cultivations. Nitrogen management has long been known to influence algae biomass productivity and biochemical composition; here, we demonstrate that it also strongly influences the stability of post-harvest algae biomass in anaerobic storage.}, }
@article {pmid36928667, year = {2023}, author = {Yokoyama, M and Peto, L and Budgell, EP and Jones, N and Sheridan, E and Liu, J and Walker, AS and Stoesser, N and Gweon, HS and Llewelyn, MJ}, title = {Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0282584}, doi = {10.1371/journal.pone.0282584}, pmid = {36928667}, issn = {1932-6203}, abstract = {Antimicrobial resistance (AMR) is a threat to global public health. However, unsatisfactory approaches to directly measuring the AMR burden carried by individuals has hampered efforts to assess interventions aimed at reducing selection for AMR. Metagenomics can provide accurate detection and quantification of AMR genes within an individual person's faecal flora (their gut "resistome"). Using this approach, we aimed to test the hypothesis that differences in antimicrobial use across different hospitals in the United Kingdom will result in observable differences in the resistome of individual patients. Three National Health Service acute Hospital Trusts with markedly different antibiotic use and Clostridioides difficile infection rates collected faecal samples from anonymous patients which were discarded after C. difficile testing over a period of 9 to 15 months. Metagenomic DNA was extracted from these samples and sequenced using an Illumina NovaSeq 6000 platform. The resulting sequencing reads were analysed for taxonomic composition and for the presence of AMR genes. Among 683 faecal metagenomes we found huge variation between individuals in terms of taxonomic diversity (Shannon Index range 0.10-3.99) and carriage of AMR genes (Median 1.50 genes/cell/sample overall). We found no statistically significant differences in diversity (median Shannon index 2.16 (IQR 1.71-2.56), 2.15 (IQR 1.62-2.50) and 2.26 (IQR 1.55-2.51)) or carriage of AMR genes (median 1.37 genes/cell/sample (IQR 0.70-3.24), 1.70 (IQR 0.70-4.52) and 1.43 (IQR 0.55-3.71)) at the three trusts respectively. This was also the case across the sample collection period within the trusts. While we have not demonstrated differences over place or time using metagenomic sequencing of faecal discards, other sampling frameworks may be more suitable to determine whether organisational level differences in antibiotic use are associated with individual-level differences in burden of AMR carriage.}, }
@article {pmid36928278, year = {2023}, author = {Okazaki, Y and Nguyen, TT and Nishihara, A and Endo, H and Ogata, H and Nakano, SI and Tamaki, H}, title = {A Fast and Easy Method to Co-extract DNA and RNA from an Environmental Microbial Sample.}, journal = {Microbes and environments}, volume = {38}, number = {1}, pages = {}, doi = {10.1264/jsme2.ME22102}, pmid = {36928278}, issn = {1347-4405}, abstract = {We herein propose a fast and easy DNA and RNA co-extraction method for environmental microbial samples. It combines bead beating and phenol-chloroform phase separation followed by the separation and purification of DNA and RNA using the Qiagen AllPrep DNA/RNA mini kit. With a handling time of ~3 h, our method simultaneously extracted high-quality DNA (peak size >10-15‍ ‍kb) and RNA (RNA integrity number >6) from lake bacterioplankton filtered samples. The method is also applicable to low-biomass samples (expected DNA or RNA yield <50‍ ‍ng) and eukaryotic microbial samples, providing an easy option for more versatile eco-genomic applications.}, }
@article {pmid36927888, year = {2023}, author = {Sadee, W and Wang, D and Hartmann, K and Toland, AE}, title = {PHARMACOGENOMICS: Driving Personalized Medicine.}, journal = {Pharmacological reviews}, volume = {}, number = {}, pages = {}, doi = {10.1124/pharmrev.122.000810}, pmid = {36927888}, issn = {1521-0081}, abstract = {Personalized medicine tailors therapies, disease prevention, and health maintenance to the individual, with pharmacogenomics serving as a key tool to improve outcomes and prevent adverse effects. Advances in genomics have transformed pharmacogenetics, traditionally focused on single gene-drug pairs, into pharmacogenomics, encompassing all 'omics' fields, e.g., proteomics, transcriptomics, metabolomics, and metagenomics. This review summarizes basic genomics principles relevant to translation into therapies, assessing pharmacogenomics' central role in converging diverse elements of personalized medicine. We discuss genetic variations in pharmacogenes (drug-metabolizing enzymes, drug transporters, and receptors), their clinical relevance as biomarkers, and the legacy of decades of research in pharmacogenetics. All types of therapies, including proteins, nucleic acids, viruses, cells, genes, and irradiation, can benefit from genomics, expanding the role of pharmacogenomics across medicine. FDA approvals of personalized therapeutics involving biomarkers increase rapidly, demonstrating the growing impact of pharmacogenomics. A beacon for all therapeutic approaches, molecularly targeted cancer therapies highlight trends in drug discovery and clinical applications. To account for human complexity, multi-component biomarker panels encompassing genetic, personal, and environmental factors can guide diagnosis and therapies, increasingly involving artificial intelligence to cope with extreme data complexities. However, clinical application encounters substantial hurdles, such as unknown validity across ethnic groups, underlying bias in health care, and real-world validation. This review will address the underlying science and technologies germane to pharmacogenomics and personalized medicine, integrated with economic, ethical, and regulatory issues - providing insights into the current status and future direction of health care. Significance Statement Personalized medicine aims to optimize health care for the individual patients with use of predictive biomarkers to improve outcomes and prevent adverse effects. Pharmacogenomics drives biomarker discovery and guides the development of targeted therapeutics. This review addresses basic principles and current trends in pharmacogenomics, with large-scale data repositories accelerating medical advances. The impact of pharmacogenomics is discussed, along with hurdles impeding broad clinical implementation, in the context of clinical care, ethics, economics, and regulatory affairs.}, }
@article {pmid36927795, year = {2023}, author = {Yi, X and Huang, C and Huang, C and Zhao, M and Lu, Q}, title = {Fecal microbiota from MRL/lpr mice exacerbates pristane-induced lupus.}, journal = {Arthritis research &amp; therapy}, volume = {25}, number = {1}, pages = {42}, pmid = {36927795}, issn = {1478-6362}, abstract = {BACKGROUND: The roles of gut microbiota in the pathogenesis of SLE have been receiving much attention during recent years. However, it remains unknown how fecal microbiota transplantation (FMT) and microbial metabolites affect immune responses and lupus progression.<br><br>METHODS: We transferred fecal microbiota from MRL/lpr (Lpr) mice and MRL/Mpj (Mpj) mice or PBS to pristane-induced lupus mice and observed disease development. We also screened gut microbiota and metabolite spectrums of pristane-induced lupus mice with FMT via 16S rRNA sequencing, metagenomic sequencing, and metabolomics, followed by correlation analysis.<br><br>RESULTS: FMT from MRL/lpr mice promoted the pathogenesis of pristane-induced lupus and affected immune cell profiles in the intestine, particularly the plasma cells. The structure and composition of microbial communities in the gut of the FMT-Lpr mice were different from those of the FMT-Mpj mice and FMT-PBS mice. The abundances of specific microbes such as prevotella taxa were predominantly elevated in the gut microbiome of the FMT-Lpr mice, which were positively associated with functional pathways such as cyanoamino acid metabolism. Differential metabolites such as valine and L-isoleucine were identified with varied abundances among the three groups. The abundance alterations of the prevotella taxa may affect the phenotypic changes such as proteinuria levels in the pristane-induced lupus mice.<br><br>CONCLUSION: These findings further confirm that gut microbiota play an important role in the pathogenesis of lupus. Thus, altering the gut microbiome may provide a novel way to treat lupus.}, }
@article {pmid36927099, year = {2023}, author = {Chen, J and Li, Y and Zhong, C and Xu, Z and Lu, G and Jing, H and Liu, H}, title = {Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0117922}, doi = {10.1128/msystems.01179-22}, pmid = {36927099}, issn = {2379-5077}, abstract = {Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.}, }
@article {pmid36927031, year = {2023}, author = {Lin, Z and Akin, H and Rao, R and Hie, B and Zhu, Z and Lu, W and Smetanin, N and Verkuil, R and Kabeli, O and Shmueli, Y and Dos Santos Costa, A and Fazel-Zarandi, M and Sercu, T and Candido, S and Rives, A}, title = {Evolutionary-scale prediction of atomic-level protein structure with a language model.}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6637}, pages = {1123-1130}, doi = {10.1126/science.ade2574}, pmid = {36927031}, issn = {1095-9203}, abstract = {Recent advances in machine learning have leveraged evolutionary information in multiple sequence alignments to predict protein structure. We demonstrate direct inference of full atomic-level protein structure from primary sequence using a large language model. As language models of protein sequences are scaled up to 15 billion parameters, an atomic-resolution picture of protein structure emerges in the learned representations. This results in an order-of-magnitude acceleration of high-resolution structure prediction, which enables large-scale structural characterization of metagenomic proteins. We apply this capability to construct the ESM Metagenomic Atlas by predicting structures for >617 million metagenomic protein sequences, including >225 million that are predicted with high confidence, which gives a view into the vast breadth and diversity of natural proteins.}, }
@article {pmid36926893, year = {2023}, author = {Shi, C and Tong, M and Cai, Q and Li, Z and Li, P and Lu, Y and Cao, Z and Liu, H and Zhao, HP and Yuan, S}, title = {Electrokinetic-Enhanced Bioremediation of Trichloroethylene-Contaminated Low-Permeability Soils: Mechanistic Insight from Spatio-Temporal Variations of Indigenous Microbial Community and Biodehalogenation Activity.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c00278}, pmid = {36926893}, issn = {1520-5851}, abstract = {Electrokinetic-enhanced bioremediation (EK-Bio), particularly bioaugmentation with injection of biodehalogenation functional microbes such as Dehalococcoides, has been documented to be effective in treating a low-permeability subsurface matrix contaminated with chlorinated ethenes. However, the spatio-temporal variations of indigenous microbial community and biodehalogenation activity of the background matrix, a fundamental aspect for understanding EK-Bio, remain unclear. To fill this gap, we investigated the variation of trichloroethylene (TCE) biodehalogenation activity in response to indigenous microbial community succession in EK-Bio by both column and batch experiments. For a 195 day EK-Bio column (∼1 V/cm, electrolyte circulation, lactate addition), biodehalogenation activity occurred first near the cathode (<60 days) and then spread to the anode (>90 days), which was controlled by electron acceptor (i.e., Fe(III)) competition and microbe succession. Amplicon sequencing and metagenome analysis revealed that iron-reducing bacteria (Geobacter, Anaeromyxobacter, Geothrix) were enriched within initial 60 d and were gradually replaced by organohalide-respiring bacteria (versatile Geobacter and obligate Dehalobacter) afterward. Iron-reducing bacteria required an initial long time to consume the competitive electron acceptors so that an appropriate reductive condition could be developed for the enrichment of organohalide-respiring bacteria and the enhancement of TCE biodehalogenation activity.}, }
@article {pmid36926836, year = {2023}, author = {Severino, R and Moreno-Paz, M and Puente-Sánchez, F and Sánchez-García, L and Risso, VA and Sanchez-Ruiz, JM and Cabrol, N and Parro, V}, title = {Immunoanalytical Approach for Detecting and Identifying Ancestral Peptide Biomarkers in Early Earth Analogue Environments.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.2c05386}, pmid = {36926836}, issn = {1520-6882}, abstract = {Several mass spectrometry and spectroscopic techniques have been used in the search for molecular biomarkers on Mars. A major constraint is their capability to detect and identify large and complex compounds such as peptides or other biopolymers. Multiplex immunoassays can detect these compounds, but antibodies must be produced for a large number of sequence-dependent molecular targets. Ancestral Sequence Reconstruction (ASR) followed by protein "resurrection" in the lab can help to narrow the selection of targets. Herein, we propose an immunoanalytical method to identify ancient and universally conserved protein/peptide sequences as targets for identifying ancestral biomarkers in nature. We have developed, tested, and validated this approach by producing antibodies to eight previously described ancestral resurrected proteins (three β-lactamases, three thioredoxins, one Elongation Factor Tu, and one RuBisCO, all of them theoretically dated as Precambrian), and used them as a proxy to search for any potential feature of them that could be present in current natural environments. By fluorescent sandwich microarray immunoassays (FSMI), we have detected positive immunoreactions with antibodies to the oldest β-lactamase and thioredoxin proteins (ca. 4 Ga) in samples from a hydrothermal environment. Fine epitope mapping and inhibitory immunoassays allowed the identification of well-conserved epitope peptide sequences that resulted from ASR and were present in the sample. We corroborated these results by metagenomic sequencing and found several genes encoding analogue proteins with significant matches to the peptide epitopes identified with the antibodies. The results demonstrated that peptides inferred from ASR studies have true counterpart analogues in Nature, which validates and strengthens the well-known ASR/protein resurrection technique and our immunoanalytical approach for investigating ancient environments and metabolisms on Earth and elsewhere.}, }
@article {pmid36926398, year = {2023}, author = {Deng, ZF and Tang, YJ and Yan, CY and Qin, ZQ and Yu, N and Zhong, XB}, title = {Pulmonary nocardiosis with bloodstream infection diagnosed by metagenomic next-generation sequencing in a kidney transplant recipient: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {7}, pages = {1634-1641}, pmid = {36926398}, issn = {2307-8960}, abstract = {BACKGROUND: Pulmonary nocardiosis is difficult to diagnose by culture and other conventional testing, and is often associated with lethal disseminated infections. This difficulty poses a great challenge to the timeliness and accuracy of clinical detection, especially in susceptible immunosuppressed individuals. Metagenomic next-generation sequencing (mNGS) has transformed the conventional diagnosis pattern by providing a rapid and precise method to assess all microorganisms in a sample.<br><br>CASE SUMMARY: A 45-year-old male was hospitalized for cough, chest tightness and fatigue for 3 consecutive days. He had received a kidney transplant 42 d prior to admission. No pathogens were detected at admission. Chest computed tomography showed nodules, streak shadows and fiber lesions in both lung lobes as well as right pleural effusion. Pulmonary tuberculosis with pleural effusion was highly suspected based on the symptoms, imaging and residence in a high tuberculosis-burden area. However, anti-tuberculosis treatment was ineffective, showing no improvement in computed tomography imaging. Pleural effusion and blood samples were subsequently sent for mNGS. The results indicated Nocardia farcinica as the major pathogen. After switching to sulphamethoxazole combined with minocycline for anti-nocardiosis treatment, the patient gradually improved and was finally discharged.<br><br>CONCLUSION: A case of pulmonary nocardiosis with an accompanying bloodstream infection was diagnosed and promptly treated before the dissemination of the infection. This report emphasizes the value of mNGS in the diagnosis of nocardiosis. mNGS may be an effective method for facilitating early diagnosis and prompt treatment in infectious diseases, which overcomes the shortcomings of conventional testing.}, }
@article {pmid36926275, year = {2023}, author = {Bertoline, LMF and Lima, AN and Krieger, JE and Teixeira, SK}, title = {Before and after AlphaFold2: An overview of protein structure prediction.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1120370}, pmid = {36926275}, issn = {2673-7647}, abstract = {Three-dimensional protein structure is directly correlated with its function and its determination is critical to understanding biological processes and addressing human health and life science problems in general. Although new protein structures are experimentally obtained over time, there is still a large difference between the number of protein sequences placed in Uniprot and those with resolved tertiary structure. In this context, studies have emerged to predict protein structures by methods based on a template or free modeling. In the last years, different methods have been combined to overcome their individual limitations, until the emergence of AlphaFold2, which demonstrated that predicting protein structure with high accuracy at unprecedented scale is possible. Despite its current impact in the field, AlphaFold2 has limitations. Recently, new methods based on protein language models have promised to revolutionize the protein structural biology allowing the discovery of protein structure and function only from evolutionary patterns present on protein sequence. Even though these methods do not reach AlphaFold2 accuracy, they already covered some of its limitations, being able to predict with high accuracy more than 200 million proteins from metagenomic databases. In this mini-review, we provide an overview of the breakthroughs in protein structure prediction before and after AlphaFold2 emergence.}, }
@article {pmid36925044, year = {2023}, author = {Baldanzi, G and Sayols-Baixeras, S and Theorell-Haglöw, J and Dekkers, KF and Hammar, U and Nguyen, D and Lin, YT and Ahmad, S and Holm, JB and Nielsen, HB and Brunkwall, L and Benedict, C and Cedernaes, J and Koskiniemi, S and Phillipson, M and Lind, L and Sundström, J and Bergström, G and Engström, G and Smith, JG and Orho-Melander, M and Ärnlöv, J and Kennedy, B and Lindberg, E and Fall, T}, title = {Obstructive sleep apnea was associated with the human gut microbiota composition and functional potential in the population-based Swedish CardioPulmonary bioImage Study (SCAPIS).}, journal = {Chest}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chest.2023.03.010}, pmid = {36925044}, issn = {1931-3543}, abstract = {BACKGROUND: Obstructive sleep apnea (OSA) is a common sleep-breathing disorder linked to increased risk of cardiovascular disease. Intermittent hypoxia and intermittent airway obstruction, hallmarks of OSA, have been shown in animal models to induce substantial changes to the gut microbiota composition and subsequent transplantation of fecal matter to other animals induced changes in blood pressure and glucose metabolism.<br><br>RESEARCH QUESTION: Does obstructive sleep apnea in adults associate with the composition and metabolic potential of the human gut microbiota?<br><br>STUDY DESIGN AND METHODS: We used respiratory polygraphy data from up to 3,570 individuals aged 50-64 from the population-based Swedish CardioPulmonary bioImage Study combined with deep shotgun metagenomics of fecal samples to identify cross-sectional associations between three OSA parameters covering apneas and hypopneas, cumulative sleep time in hypoxia and number of oxygen desaturation events with gut microbiota composition. Data collection about potential confounders was based on questionnaires, on-site anthropometric measurements, plasma metabolomics, and linkage with the Swedish Prescribed Drug Register.<br><br>RESULTS: We found that all three OSA parameters were associated with lower diversity of species in the gut. Further, the OSA-related hypoxia parameters were in multivariable-adjusted analysis associated with the relative abundance of 128 gut bacterial species, including higher abundance of Blautia obeum and Collinsela aerofaciens. The latter species was also independently associated with increased systolic blood pressure. Further, the cumulative time in hypoxia during sleep was associated with the abundance of genes involved in nine gut microbiota metabolic pathways, including propionate production from lactate. Lastly, we observed two heterogeneous sets of plasma metabolites with opposite association with species positively and negatively associated with hypoxia parameters, respectively.<br><br>INTERPRETATION: OSA-related hypoxia, but not the number of apneas/hypopneas, is associated with specific gut microbiota species and functions. Our findings lay the foundation for future research on the gut microbiota-mediated health effects of OSA.}, }
@article {pmid36925017, year = {2023}, author = {Liu, YY and Zhang, YX and Wen, HM and Liu, XL and Fan, XJ}, title = {Cloning and rational modification of a cold-adapted esterase for phthalate esters and parabens degradation.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {138393}, doi = {10.1016/j.chemosphere.2023.138393}, pmid = {36925017}, issn = {1879-1298}, abstract = {Phthalate esters (PAEs) and parabens are environmental pollutants that can be toxic to human health. Herein, a cold-adapted esterase from the Mao-tofu metagenome named Est1260 was screened for its PAE-hydrolyzing potential in cold temperatures. The results showed that purified Est1260 could degrade a variety of PAEs and parabens at temperatures as low as 0 °C. After careful analysis of the structural information and molecular docking, site-saturation mutation was conducted at the identified hotspots. Protein expression of variant A1B6 doubled, and its thermal stability significantly improved (24 times) without sacrificing activity at low temperatures. In addition, Est1260 and its variants were activated by NaCl and demonstrated resistance to high concentrations of saline (up to 5 M), making it a potential biocatalyst for bioremediation of PAE and paraben-polluted environments.}, }
@article {pmid36923821, year = {2023}, author = {Homayouni, R and Manda, P and Tan, AC and Qin, ZS}, title = {Editorial: AI and data science in drug development and public health: Highlights from the MCBIOS 2022 conference.}, journal = {Frontiers in big data}, volume = {6}, number = {}, pages = {1156811}, doi = {10.3389/fdata.2023.1156811}, pmid = {36923821}, issn = {2624-909X}, }
@article {pmid36923492, year = {2023}, author = {Peng, Y and Chiu, ATG and Li, VWY and Zhang, X and Yeung, WL and Chan, SHS and Tun, HM}, title = {The role of the gut-microbiome-brain axis in metabolic remodeling amongst children with cerebral palsy and epilepsy.}, journal = {Frontiers in neurology}, volume = {14}, number = {}, pages = {1109469}, pmid = {36923492}, issn = {1664-2295}, abstract = {BACKGROUND: Epilepsy-associated dysbiosis in gut microbiota has been previously described, but the mechanistic roles of the gut microbiome in epileptogenesis among children with cerebral palsy (CP) have yet to be illustrated.<br><br>METHODS: Using shotgun metagenomic sequencing coupled with untargeted metabolomics analysis, this observational study compared the gut microbiome and metabolome of eight children with non-epileptic cerebral palsy (NECP) to those of 13 children with cerebral palsy with epilepsy (CPE). Among children with CPE, 8 had drug-sensitive epilepsy (DSE) and five had drug-resistant epilepsy (DRE). Characteristics at enrollment, medication history, and 7-day dietary intake were compared between groups.<br><br>RESULTS: At the species level, CPE subjects had significantly lower abundances of Bacteroides fragilis and Dialister invisus but higher abundances of Phascolarctobacterium faecium and Eubacterium limosum. By contrast, DRE subjects had a significantly higher colonization of Veillonella parvula. Regarding microbial functional pathways, CPE subjects had decreased abundances of pathways for serine degradation, quinolinic acid degradation, glutamate degradation I, glycerol degradation, sulfate reduction, and nitrate reduction but increased abundances of pathways related to ethanol production. As for metabolites, CPE subjects had higher concentrations of kynurenic acid, 2-oxindole, dopamine, 2-hydroxyphenyalanine, 3,4-dihydroxyphenylglycol, L-tartaric acid, and D-saccharic acid; DRE subjects had increased concentrations of indole and homovanilic acid.<br><br>CONCLUSIONS: In this study, we found evidence of gut dysbiosis amongst children with cerebral palsy and epilepsy in terms of gut microbiota species, functional pathways, and metabolites. The combined metagenomic and metabolomic analyses have shed insights on the potential roles of B. fragilis and D. invisus in neuroprotection. The combined analyses have also provided evidence for the involvement of GMBA in the epilepsy-related dysbiosis of kynurenine, serotonin, and dopamine pathways and their complex interplay with neuroimmune and neuroendocrinological pathways.}, }
@article {pmid36922970, year = {2023}, author = {Zeng, Y and Cao, S and Yang, H}, title = {Roles of gut microbiome in epilepsy risk: A Mendelian randomization study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1115014}, pmid = {36922970}, issn = {1664-302X}, abstract = {BACKGROUND: Recent studies have suggested an association between gut microbiomes (GMs) and epilepsy. However, the GM taxa identified in different studies are variable. In addition, observational studies cannot indicate causality. Therefore, our study aimed to explore the causal association of GMs with epilepsy and identify the most influential GM taxa.<br><br>METHODS: We conducted a Mendelian randomization (MR) study using summary statistics from genome-wide association studies (GWAS) of 211 GM taxa and epilepsy. The GWAS summary statistics for 211 GM taxa (from phylum to genus level) were generated by the MiBioGen consortium, while the FinnGen consortium provided the GWAS summary statistics for epilepsy. The primary analytical method to assess causality was the inverse-variance weighted (IVW) approach. To complement the IVW method, we also applied four additional MR methods: MR-Egger, weighted median, simple mode, and weighted. In addition, we conducted sensitivity analyses using Cochrane's Q-test, MR-Egger intercept test, MR-PRESSO global test, and leave-one-out analysis.<br><br>RESULTS: We evaluated the causal effect of 211 GM taxa (from phylum to genus level) on epilepsy, generalized epilepsy, and focal epilepsy. After using the Bonferroni method for multiple testing correction, Class Betaproteobacteria [odds ratio (OR)&#x2009;=&#x2009;1.357, 95% confidence interval (CI): 1.126-1.635, p&#x2009;=&#x2009;0.001] and Order Burkholderiales (OR&#x2009;=&#x2009;1.336, 95% CI: 1.112-1.606, p =&#x2009;0.002). In addition, 21 nominally significant causal relationships were also identified. Further, the MR-Egger intercept test and MR-PRESSO global test suggested that our MR analysis was unaffected by horizontal pleiotropy (p&#x2009;>&#x2009;0.05). Finally, the leave-one-out analysis suggested the robustness of the results.<br><br>CONCLUSION: Through the MR study, we analyzed the causal relationship of 211 GM taxa with epilepsy and determined the specific intestinal flora associated with increased epilepsy risk. Our findings may provide helpful biomarkers for disease progression and potential candidate therapeutic targets for epilepsy. In addition, in-depth analysis of large-scale microbiome GWAS datasets based on metagenomics sequencing is necessary for future studies.}, }
@article {pmid36922966, year = {2023}, author = {Kalntremtziou, M and Papaioannou, IA and Vangalis, V and Polemis, E and Pappas, KM and Zervakis, GI and Typas, MA}, title = {Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1121993}, pmid = {36922966}, issn = {1664-302X}, abstract = {The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.}, }
@article {pmid36922761, year = {2023}, author = {Marynowska, M and Sillam-Dussès, D and Untereiner, B and Klimek, D and Goux, X and Gawron, P and Roisin, Y and Delfosse, P and Calusinska, M}, title = {A holobiont approach towards polysaccharide degradation by the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {115}, pmid = {36922761}, issn = {1471-2164}, abstract = {BACKGROUND: Termites are among the most successful insects on Earth and can feed on a broad range of organic matter at various stages of decomposition. The termite gut system is often referred to as a micro-reactor and is a complex structure consisting of several components. It includes the host, its gut microbiome and fungal gardens, in the case of fungi-growing higher termites. The digestive tract of soil-feeding higher termites is characterised by radial and axial gradients of physicochemical parameters (e.g. pH, O2 and H2 partial pressure), and also differs in the density and structure of residing microbial communities. Although soil-feeding termites account for 60% of the known termite species, their biomass degradation strategies are far less known compared to their wood-feeding counterparts.<br><br>RESULTS: In this work, we applied an integrative multi-omics approach for the first time at the holobiont level to study the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis. We relied on 16S rRNA gene community profiling, metagenomics and (meta)transcriptomics to uncover the distribution of functional roles, in particular those related to carbohydrate hydrolysis, across different gut compartments and among the members of the bacterial community and the host itself. We showed that the Labiotermes gut was dominated by members of the Firmicutes phylum, whose abundance gradually decreased towards the posterior segments of the hindgut, in favour of Bacteroidetes, Proteobacteria and Verrucomicrobia. Contrary to expectations, we observed that L. labralis gut microbes expressed a high diversity of carbohydrate active enzymes involved in cellulose and hemicelluloses degradation, making the soil-feeding termite gut a unique reservoir of lignocellulolytic enzymes with considerable biotechnological potential. We also evidenced that the host cellulases have different phylogenetic origins and structures, which is possibly translated into their different specificities towards cellulose. From an ecological perspective, we could speculate that the capacity to feed on distinct polymorphs of cellulose retained in soil might have enabled this termite species to widely colonise the different habitats of the Amazon basin.<br><br>CONCLUSIONS: Our study provides interesting insights into the distribution of the hydrolytic potential of the highly compartmentalised higher termite gut. The large number of expressed enzymes targeting the different lignocellulose components make the Labiotermes worker gut a relevant lignocellulose-valorising model to mimic by biomass conversion industries.}, }
@article {pmid36922730, year = {2023}, author = {Omori, M and Kato-Kogoe, N and Sakaguchi, S and Komori, E and Inoue, K and Yamamoto, K and Hamada, W and Hayase, T and Tano, T and Nakamura, S and Nakano, T and Une, H and Ueno, T}, title = {Characterization of Oral Microbiota Following Chemotherapy in Patients With Hematopoietic Malignancies.}, journal = {Integrative cancer therapies}, volume = {22}, number = {}, pages = {15347354231159309}, doi = {10.1177/15347354231159309}, pmid = {36922730}, issn = {1552-695X}, abstract = {Oral microbiota may be associated with serious local or systemic medical conditions resulting from chemotherapy. This study was conducted to evaluate the changes in the oral microbiota following the initiation of chemotherapy in patients with hematopoietic malignancies and to identify the characteristics of the oral microbiota associated with oral mucositis. Oral samples were collected from 57 patients with hematopoietic malignancies at 2 time points: before the start of chemotherapy and 8 to 20 days after the start of chemotherapy, when chemotherapy-induced oral mucositis often occurs, and 16S rRNA metagenomic analyses were performed. Comparative and linear discriminant analysis effect size (LEfSe) analyses were used to determine the characteristic bacterial groups before and after the initiation of chemotherapy and in those who developed oral mucositis. The alpha and beta diversities of oral microbiota before and after the initiation of chemotherapy differed significantly (operational taxonomic unit index, P < .001; Shannon's index, P < .001; unweighted UniFrac distances, P = .001; and weighted UniFrac distances, P = .001). The LEfSe analysis revealed a group of bacteria whose abundance differed significantly before and after the initiation of chemotherapy. In the group of patients who developed oral mucositis, a characteristic group of bacteria was identified before the start of chemotherapy. In conclusion, we characterized the oral microbiota associated with the initiation of chemotherapy in patients with hematopoietic malignancies. In addition, our findings suggest that oral microbiota composition before the start of chemotherapy may be associated with oral mucositis. The results of this study emphasize the importance of oral management focusing on the oral microbiota during chemotherapy in patients with hematologic malignancies.}, }
@article {pmid36922572, year = {2023}, author = {Michishita, R and Shimoda, M and Furukawa, S and Uehara, T}, title = {Inoculation with black soldier fly larvae alters the microbiome and volatile organic compound profile of decomposing food waste.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4297}, pmid = {36922572}, issn = {2045-2322}, abstract = {The black soldier fly (BSF; Hermetia illucens) is used in sustainable processing of many types of organic waste. However, organic waste being decomposed by BSF produces strong odors, hindering more widespread application. The odor components and how they are produced have yet to be characterized. We found that digestion of food waste by BSF significantly alters the microbial flora, based on metagenomic analyses, and the odor components generated, as shown by thermal desorption gas chromatography mass spectrometry analysis. Inoculation with BSF significantly decreased production of volatile organic sulfur compounds (dimethyl disulfide and dimethyl trisulfide), which are known to be released during methionine and cysteine metabolism by Lactobacillus and Enterococcus bacteria. BSF inoculation significantly changed the abundance of Lactobacillus and Enterococcus and decreased microbial diversity overall. These findings may help in optimizing use of BSF for deodorization of composting food waste.}, }
@article {pmid36922385, year = {2023}, author = {Yang, S and Fan, Z and Li, J and Wang, X and Lan, Y and Yue, B and He, M and Zhang, A and Li, J}, title = {Assembly of novel microbial genomes from gut metagenomes of rhesus macaque (Macaca mulatta).}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2188848}, doi = {10.1080/19490976.2023.2188848}, pmid = {36922385}, issn = {1949-0984}, abstract = {Rhesus macaque (RM, Macaca mulatta), as an important model animal, commonly suffers from chronic diarrheal disease, challenging the breeding of RMs. Gut microbiomes play key roles in maintaining intestinal health of RMs. However, it is still unclear about more features of gut microbiome as responsible for intestinal health of RMs. In this study, we performed de novo assembly of metagenome-assembled genomes (MAGs) based on fecal metagenomes from chronic diarrheal RMs and asymptomatic individuals. In total of 731 non-redundant MAGs with at least 80% completeness were reconstructed in this study. More than 97% MAGs were novel genomes compared with more than 250,000 reference genomes. MAGs of Campylobacter and Helicobacteraceae from RM guts mainly carried flagella-associated virulence genes and chemotaxis-associated virulence genes, which might mediate motility and adhesion of bacteria. Comparing to MAGs of Campylobacter from humans, distributions and functions of these MAGs of Campylobacter from RMs exhibited significant differences. Most members of Bacteroidota, Spirochaetota, Helicobacteraceae, Lactobacillaceae and Anaerovibrio significantly decreased in guts of chronic diarrhea RMs. More than 92% MAGs in this study were not contained in 2,985 MAGs previously reported from other 22 non-human primates (NHPs), expanding the microbial diversity in guts of NHPs. The distributions and functions of gut microbiome were prominently influenced by host phylogeny of NHPs. Our results could help to more clearly understand about the diversity and function of RMs gut microbiome.}, }
@article {pmid36922214, year = {2023}, author = {Liu, CX and Bai, XH}, title = {[Distribution Characteristics of Antibiotic Resistance Genes on Different Water Supply Pipes].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {3}, pages = {1537-1541}, doi = {10.13227/j.hjkx.202204208}, pmid = {36922214}, issn = {0250-3301}, abstract = {To study the distribution characteristics and horizontal transfer potential of antibiotic resistance genes in biofilms of water supply pipes made of different materials, the biofilms of 304 and 316 L stainless steel pipes and PPR and PE plastic pipes were analyzed using metagenomic sequencing. The results showed that a total of 146 antibiotic resistance genes belonging to 17 classes were detected in the biofilms. Multidrug resistance genes had the highest abundance and varied a lot in different biofilms, which was the main reason for the differences in antibiotic resistance genes in different biofilms. The total abundance of mobile genetic elements was high in different biofilms, but overall coexistence with antibiotic resistance genes was low, with integrase genes showing a closer relationship with antibiotic resistance genes and possibly playing an important role in the horizontal transfer of antibiotic resistance genes. Different antibiotic resistance genes possessed different genera of potential hosts; highly abundant hosts such as Aquabacterium and Bradyrhizobium were the basis for the presence of a high abundance of multidrug resistance genes. Microbial attachment in different pipe walls was selective, and the primary influence of antibiotic resistance in biofilms was bacterial community composition, followed by the horizontal transfer of genes mediated by mobile genetic elements, community composition, and mobile genetic elements together shaping the distribution characteristics of antibiotic resistance genes.}, }
@article {pmid36921777, year = {2023}, author = {Li, P and Chen, CZ and Zhao, XL and Liu, L and Li, ZH}, title = {Metagenomics analysis reveals the effects of norfloxacin on the gut microbiota of juvenile common carp (Cyprinus carpio).}, journal = {Chemosphere}, volume = {}, number = {}, pages = {138389}, doi = {10.1016/j.chemosphere.2023.138389}, pmid = {36921777}, issn = {1879-1298}, abstract = {Norfloxacin (NOR) is an early third-generation quinolone antibiotic that has been widely used in animal husbandry and aquaculture because of its bactericidal properties. As an emerging contaminant, NOR may have toxic effects on fish. This study assessed the chronic toxicity (6 weeks) of 0 (control group), 100 ng/L (environmental concentration), and 1 mg/L NOR to the gut microbiota of juvenile common carp (Cyprinus carpio) based on metagenomic sequencing. Metagenomic analysis revealed that the Proteobacteria, Bacteroidetes, Fusobacteria, Firmicutes, and Actinobacteria were the dominant bacteria in the gut of common carp. The relative abundance of Actinobacteria was highest in the control group. The alpha diversity of the environmental concentration NOR was significantly lower than the control group. Principal coordinates analysis (PCoA) indicated that the bacterial community between the different groups formed clear separate clusters. NOR exposure adversely could affect immune function and some substance metabolic pathways in the gut microbiota of common carp. Furthermore, environmental concentrations of NOR produce antibiotic resistance genes (ARGs) in the gut microbiota, enhancing resistance to drugs. In conclusion, environmental concentrations of NOR could alter the composition, structure, and abundance of ARGs in the gut microbiota, thereby affecting the intestinal health of fish.}, }
@article {pmid36921697, year = {2023}, author = {Tsz Long Wong, D and Norman, H and Creedy, TJ and Jordaens, K and Moran, KM and Young, A and Mengual, X and Skevington, JH and Vogler, AP}, title = {The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {107759}, doi = {10.1016/j.ympev.2023.107759}, pmid = {36921697}, issn = {1095-9513}, abstract = {Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to allow such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies.}, }
@article {pmid36921549, year = {2023}, author = {Bortoluzzi, C and Tamburini, I and Geremia, J}, title = {Microbiome modulation, microbiome protein metabolism index, and growth performance of broilers supplemented with a precision biotic.}, journal = {Poultry science}, volume = {102}, number = {5}, pages = {102595}, doi = {10.1016/j.psj.2023.102595}, pmid = {36921549}, issn = {1525-3171}, abstract = {The objectives of the present studies were to evaluate: 1) the in vivo impact of the supplementation with a precision biotic (PB) on the growth performance and microbiome modulation of broiler chickens; 2) the role of PB on the modulation of functional pathways of the microbiome collected from animals with low and high body weight gain, and 3) to develop a Microbiome Protein Metabolism Index (MPMI) derived from gut metagenomic data to link microbial protein metabolism with performance. The in vivo work consisted of 2 experiments with 2 treatments: Control vs. PB at 1.1 kg/MT of PB with 21 or 14 replicates of 40 birds per replicate, in experiments 1 and 2, respectively. Growth performance was evaluated in both experiments, and from experiment 1, cecal samples from one bird/replicate was collected on d 21 and 42 (n = 21/treatment) to evaluate the microbiome through whole genome sequencing. In the ex vivo assay, 6 cecal samples were collected from low body weight (BW) birds (at 10% below average), and 6 samples from high BW birds (at least 10% above average). The samples were incubated in the presence or absence of PB. After incubation, DNA was isolated to develop a functional genomic assay and the supernatant was separated to measure short-chain fatty acid (SCFA) production. The MPMI is the sum of beneficial genes in the pathways related to protein metabolism. In the in vivo grow out experiments, it was observed that the supplementation improved the BW gain by 3% in both studies, and the corrected feed conversion ratio (cFCR) by 3.7 and 3.4% in studies 1 and 2, respectively (P < 0.05). The functional microbiome analysis revealed that the PB shifted the microbiome pathways toward a beneficial increase in protein utilization, as shown by higher MPMI. In the ex vivo experiment, the PB increased the abundance of genes related to the beneficial metabolism of protein (quantitative MPMI), and the concentration of SCFA, regardless of the underline BW of the birds. Taken together, the microbiome metabolic shift observed in the in vivo study and higher MPMI, plus the observations from the ex vivo assay with higher SFCA production, may explain the improvement in growth performance obtained with the supplementation of PB.}, }
@article {pmid36921415, year = {2023}, author = {Chen, B and Zhang, Z and Wang, T and Hu, H and Qin, G and Lu, T and Hong, W and Hu, J and Penuelas, J and Qian, H}, title = {Global distribution of marine microplastics and potential for biodegradation.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131198}, doi = {10.1016/j.jhazmat.2023.131198}, pmid = {36921415}, issn = {1873-3336}, abstract = {Microplastics are a growing marine environmental concern globally due to their high abundance and persistent degradation. We created a global map for predicting marine microplastic pollution using a machine-learning model based on 9445 samples and found that microplastics converged in zones of accumulation in subtropical gyres and near polar seas. The predicted global potential for the biodegradation of microplastics in 1112 metagenome-assembled genomes from 485 marine metagenomes indicated high potential in areas of high microplastic pollution, such as the northern Atlantic Ocean and the Mediterranean Sea. However, the limited number of samples hindered our prediction, a priority issue that needs to be addressed in the future. We further identified hosts with microplastic degradation genes (MDGs) and found that Proteobacteria accounted for a high proportion of MDG hosts, mainly Alphaproteobacteria and Gammaproteobacteria, with host-specific patterns. Our study is essential for raising awareness, identifying areas with microplastic pollution, providing a prediction method of machine learning to prioritize surveillance, and identifying the global potential of marine microbiomes to degrade microplastics, providing a reference for selecting bacteria that have the potential to degrade microplastics for further applied research.}, }
@article {pmid36920617, year = {2023}, author = {Kumar, R and Yadav, G and Kuddus, M and Ashraf, GM and Singh, R}, title = {Unlocking the microbial studies through computational approaches: how far have we reached?.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36920617}, issn = {1614-7499}, abstract = {The metagenomics approach accelerated the study of genetic information from uncultured microbes and complex microbial communities. In silico research also facilitated an understanding of protein-DNA interactions, protein-protein interactions, docking between proteins and phyto/biochemicals for drug design, and modeling of the 3D structure of proteins. These in silico approaches provided insight into analyzing pathogenic and nonpathogenic strains that helped in the identification of probable genes for vaccines and antimicrobial agents and comparing whole-genome sequences to microbial evolution. Artificial intelligence, more precisely machine learning (ML) and deep learning (DL), has proven to be a promising approach in the field of microbiology to handle, analyze, and utilize large data that are generated through nucleic acid sequencing and proteomics. This enabled the understanding of the functional and taxonomic diversity of microorganisms. ML and DL have been used in the prediction and forecasting of diseases and applied to trace environmental contaminants and environmental quality. This review presents an in-depth analysis of the recent application of silico approaches in microbial genomics, proteomics, functional diversity, vaccine development, and drug design.}, }
@article {pmid36920536, year = {2023}, author = {Kazarina, A and Kuzmicka, J and Bortkevica, S and Zayakin, P and Kimsis, J and Igumnova, V and Sadovska, D and Freimane, L and Kivrane, A and Namina, A and Capligina, V and Poksane, A and Ranka, R}, title = {Oral microbiome variations related to ageing: possible implications beyond oral health.}, journal = {Archives of microbiology}, volume = {205}, number = {4}, pages = {116}, pmid = {36920536}, issn = {1432-072X}, abstract = {The global population is getting older due to a combination of longer life expectancy and declining birth rates. Growing evidence suggests that the oral microbiota composition and distribution may have a profound effect on how well we age. The purpose of this study was to investigate age-related oral microbiome variations of supragingival plaque and buccal mucosa samples in the general population in Latvia. Our results indicated significant difference between supragingival plaque bacterial profiles of three age groups (20-40; 40-60; 60 + years). Within supragingival plaque samples, age group 20-40 showed the highest bacterial diversity with a decline during the 40-60 age period and uprise again after the age of 60. Among other differences, the important oral commensal Neisseria had declined after the age of 40. Additionally, prevalence of two well-documented opportunistic pathogens Streptococcus anginosus and Gemella sanguinis gradually rose with age within our samples. Furthermore, supragingival plaque and buccal mucosa samples significantly differed in overall bacterial composition.}, }
@article {pmid36920238, year = {2023}, author = {Kallner, A and Debelius, J and Schuppe-Koistinen, I and Pereira, M and Engstrand, L}, title = {Effects of Consuming Fermented Fish (Surströmming) on the Fecal Microflora in Healthy Individuals.}, journal = {Journal of medicinal food}, volume = {26}, number = {3}, pages = {185-192}, doi = {10.1089/jmf.2021.0195}, pmid = {36920238}, issn = {1557-7600}, abstract = {Surströmming, a Swedish fermented fish, loved by some and avoided by others, occurs in many reports on improved or cured gastrointestinal problems even by a single meal. We tested the hypothesis that the microbes of the fermented food might have a potency to modify the gut microbiome. Two groups of voluntary participants (11 male, 8 female; aged 20-80 years) were exposed to a single meal containing the fish. A 7-day dietary intervention was carried out comprising the fish as the main source of protein in a single adult. The microbiome was characterized using 16S rRNA and metagenomic sequencing. Individual community-level changes in the microbiome were compared, as well as the presence of bacteria associated with the fermented fish. We focused on Shannon alpha and UniFrac beta diversity. We did not detect any global changes in the gut microbiome in response to Surströmming, nor were we able to recover and identify any members of Halanaerobium, which were associated with and abundant in the ingested fish, in the stool samples of the participants. Our results suggest that Surströmming consumption does not alter the microbiome of healthy individuals. However, beneficial effects on a diseased gut, impaired gut microbiome, or other effects in disease remain to be studied.}, }
@article {pmid36920198, year = {2023}, author = {Muratore, D and Bertagnolli, AD and Bristow, LA and Thamdrup, B and Weitz, JS and Stewart, FJ}, title = {Microbial and Viral Genome and Proteome Nitrogen Demand Varies across Multiple Spatial Scales within a Marine Oxygen Minimum Zone.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0109522}, doi = {10.1128/msystems.01095-22}, pmid = {36920198}, issn = {2379-5077}, abstract = {Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example, by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to those of their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter-level, and even micron-level, spatial scales. It is unclear whether such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions, distinguishing free-living microbes versus particle-associated microbes. We find a substantial increase in the nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in the modulation of the C:N ratios of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes that are involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers. IMPORTANCE The genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability being known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example, along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to the interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses by using metagenomes from the nitracline of the eastern tropical North Pacific OMZ, including both particle-associated and nonassociated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micrometer to millimeter scale associated with particle-associated versus free-living lifestyles.}, }
@article {pmid36918963, year = {2023}, author = {Faist, H and Trognitz, F and Antonielli, L and Symanczik, S and White, PJ and Sessitsch, A}, title = {Potato root-associated microbiomes adapt to combined water and nutrient limitation and have a plant genotype-specific role for plant stress mitigation.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {18}, pmid = {36918963}, issn = {2524-6372}, abstract = {BACKGROUND: Due to climate change and reduced use of fertilizers combined stress scenarios are becoming increasingly frequent in crop production. In a field experiment we tested the effect of combined water and phosphorus limitation on the growth performance and plant traits of eight tetraploid and two diploid potato varieties as well as on root-associated microbiome diversity and functional potential. Microbiome and metagenome analysis targeted the diversity and potential functions of prokaryotes, fungi, plasmids, and bacteriophages and was linked to plant traits like tuber yield or timing of canopy closure.<br><br>RESULTS: The different potato genotypes responded differently to the combined stress and hosted distinct microbiota in the rhizosphere and the root endosphere. Proximity to the root, stress and potato genotype had significant effects on bacteria, whereas fungi were only mildly affected. To address the involvement of microbial functions, we investigated well and poorly performing potato genotypes (Stirling and Desir&#xe9;e, respectively) under stress conditions and executed a metagenome analysis of rhizosphere microbiomes subjected to stress and no stress conditions. Functions like ROS detoxification, aromatic amino acid and terpene metabolism were enriched and in synchrony with the metabolism of stressed plants. In Desir&#xe9;e, Pseudonocardiales had the genetic potential to take up assimilates produced in the fast-growing canopy and to reduce plant stress-sensing by degrading ethylene, but overall yield losses were high. In Stirling, Xanthomonadales had the genetic potential to reduce oxidative stress and to produce biofilms, potentially around roots. Biofilm formation could be involved in drought resilience and nutrient accessibility of Stirling and explain the recorded low yield losses. In the rhizosphere exposed to combined stress, the relative abundance of plasmids was reduced, and the diversity of phages was enriched. Moreover, mobile elements like plasmids and phages were affected by combined stresses in a genotype-specific manner.<br><br>CONCLUSION: Our study gives new insights into the interconnectedness of root-associated microbiota and plant stress responses in the field. Functional genes in the metagenome, phylogenetic composition and mobile elements play a role in potato stress adaption. In a poor and a well performing potato genotype grown under stress conditions, distinct functional genes pinpoint to a distinct stress sensing, water availability and compounds in the rhizospheres.}, }
@article {pmid36917925, year = {2023}, author = {Wang, J and Wang, C and Chu, YX and Tian, G and He, R}, title = {Characterization of methanotrophic community and activity in landfill cover soils under dimethyl sulfide stress.}, journal = {Waste management (New York, N.Y.)}, volume = {161}, number = {}, pages = {263-274}, doi = {10.1016/j.wasman.2023.02.017}, pmid = {36917925}, issn = {1879-2456}, abstract = {Landfill cover soil is the environmental interface between landfills and the atmosphere and plays an important role in mitigating CH4 emission from landfills. Here, stable isotope probing microcosms with CH4 or CH4 and dimethyl sulfide (DMS) were carried out to characterize activity and community structure of methanotrophs in landfill cover soils under DMS stress. The CH4 oxidation activity in the landfill cover soils was not obviously influenced at the DMS concentration of 0.05%, while it was inhibited at the DMS concentrations of 0.1% and 0.2%. DMS-S was mainly oxidized to sulfate (SO4[2-]) in the landfill cover soils. In the landfill cover soils, DMS could inhibit the expression of bacteria and decrease the abundances of pmoA and mmoX genes, while it could prompt the expression of pmoA and mmoX genes. γ-Proteobacteria methanotrophs including Methylocaldum, Methylobacter, Crenothrix and unclassified Methylococcaceae and α-Proteobacteria methanotrophs Methylocystis dominated in assimilating CH4 in the landfill cover soils. Of them, Methylobacter and Crenothrix had strong tolerance to DMS or DMS could promote the growth and activity of Methylobacter and Crenothrix, while Methylocaldum had weak tolerance to DMS and showed an inhibitory effect. Metagenomic analyses showed that methanotrophs had the genes of methanethiol oxidation and could metabolize CH4 and methanethiol simultaneously in the landfill cover soils. These findings suggested that methanotrophs might metabolize sulfur compounds in the landfill cover soils, which may provide the potential application in engineering for co-removal of CH4 and sulfur compounds.}, }
@article {pmid36917471, year = {2023}, author = {Zhang, Z and Yang, C and Veldsman, WP and Fang, X and Zhang, L}, title = {Benchmarking genome assembly methods on metagenomic sequencing data.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbad087}, pmid = {36917471}, issn = {1477-4054}, abstract = {Metagenome assembly is an efficient approach to reconstruct microbial genomes from metagenomic sequencing data. Although short-read sequencing has been widely used for metagenome assembly, linked- and long-read sequencing have shown their advancements in assembly by providing long-range DNA connectedness. Many metagenome assembly tools were developed to simplify the assembly graphs and resolve the repeats in microbial genomes. However, there remains no comprehensive evaluation of metagenomic sequencing technologies, and there is a lack of practical guidance on selecting the appropriate metagenome assembly tools. This paper presents a comprehensive benchmark of 19 commonly used assembly tools applied to metagenomic sequencing datasets obtained from simulation, mock communities or human gut microbiomes. These datasets were generated using mainstream sequencing platforms, such as Illumina and BGISEQ short-read sequencing, 10x Genomics linked-read sequencing, and PacBio and Oxford Nanopore long-read sequencing. The assembly tools were extensively evaluated against many criteria, which revealed that long-read assemblers generated high contig contiguity but failed to reveal some medium- and high-quality metagenome-assembled genomes (MAGs). Linked-read assemblers obtained the highest number of overall near-complete MAGs from the human gut microbiomes. Hybrid assemblers using both short- and long-read sequencing were promising methods to improve both total assembly length and the number of near-complete MAGs. This paper also discussed the running time and peak memory consumption of these assembly tools and provided practical guidance on selecting them.}, }
@article {pmid36917216, year = {2023}, author = {Houston, H and Wilson, AJ and Stone, N}, title = {Approach to the diagnosis of invasive fungal infections of the respiratory tract in the immunocompromised host.}, journal = {Current opinion in pulmonary medicine}, volume = {}, number = {}, pages = {}, doi = {10.1097/MCP.0000000000000955}, pmid = {36917216}, issn = {1531-6971}, abstract = {PURPOSE OF REVIEW: The burden of invasive fungal infection is increasing worldwide, largely due to a growing population at-risk. Most serious human fungal pathogens enter the host via the respiratory tract. Early identification and treatment of invasive fungal respiratory infections (IFRIs) in the immunocompromised host saves lives. However, their accurate diagnosis is a difficult challenge for clinicians and mortality remains high.<br><br>RECENT FINDINGS: This article reviews IFRIs, focussing on host susceptibility factors, clinical presentation, and mycological diagnosis. Several new diagnostic tools are coming of age including molecular diagnostics and point-of-care antigen tests. As diagnosis of IFRI relies heavily on invasive procedures like bronchoalveolar lavage and lung biopsy, several novel noninvasive diagnostic techniques are in development, such as metagenomics, 'volatilomics' and advanced imaging technologies.<br><br>SUMMARY: Where IFRI cannot be proven, clinicians must employ a 'weights-of-evidence' approach to evaluate host factors, clinical and mycological data. Implementation studies are needed to understand how new diagnostic tools can be best applied within clinical pathways. Differentiating invasive infection from colonization and identifying antifungal resistance remain key challenges. As our diagnostic arsenal expands, centralized clinical mycology laboratories and efforts to ensure access to new diagnostics in low-resource settings will become increasingly important.}, }
@article {pmid36917170, year = {2023}, author = {Wang, X and Wang, T and Xie, Z and Zhang, Y and Xia, S and Sun, R and He, X and Xiang, R and Zheng, Q and Liu, Z and Wang, J and Wu, H and Jin, X and Chen, W and Li, D and He, Z}, title = {GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbad092}, pmid = {36917170}, issn = {1477-4054}, abstract = {Metagenomic sequencing (mNGS) is a powerful diagnostic tool to detect causative pathogens in clinical microbiological testing owing to its unbiasedness and substantially reduced costs. Rapid and accurate classification of metagenomic sequences is a critical procedure for pathogen identification in dry-lab step of mNGS test. However, clinical practices of the testing technology are hampered by the challenge of classifying sequences within a clinically relevant timeframe. Here, we present GPMeta, a novel GPU-accelerated approach to ultrarapid pathogen identification from complex mNGS data, allowing users to bypass this limitation. Using mock microbial community datasets and public real metagenomic sequencing datasets from clinical samples, we show that GPMeta has not only higher accuracy but also significantly higher speed than existing state-of-the-art tools such as Bowtie2, Bwa, Kraken2 and Centrifuge. Furthermore, GPMeta offers GPMetaC clustering algorithm, a statistical model for clustering and rescoring ambiguous alignments to improve the discrimination of highly homologous sequences from microbial genomes with average nucleotide identity >95%. GPMetaC exhibits higher precision and recall rate than others. GPMeta underlines its key role in the development of the mNGS test in infectious diseases that require rapid turnaround times. Further study will discern how to best and easily integrate GPMeta into routine clinical practices. GPMeta is freely accessible to non-commercial users at https://github.com/Bgi-LUSH/GPMeta.}, }
@article {pmid36916946, year = {2023}, author = {Li, SH and Kang, I and Cho, JC}, title = {Metabolic Versatility of the Family Halieaceae Revealed by the Genomics of Novel Cultured Isolates.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0387922}, doi = {10.1128/spectrum.03879-22}, pmid = {36916946}, issn = {2165-0497}, abstract = {The family Halieaceae (OM60/NOR5 clade) is a gammaproteobacterial group abundant and cosmopolitan in coastal seawaters and plays an important role in response to phytoplankton blooms. However, the ecophysiology of this family remains understudied because of the vast gap between phylogenetic diversity and cultured representatives. Here, using six pure cultured strains isolated from coastal seawaters, we performed in-depth genomic analyses to provide an overview of the phylogeny and metabolic capabilities of this family. The combined analyses of 16S rRNA genes, genome sequences, and functional genes relevant to taxonomy demonstrated that each strain represents a novel species. Notably, two strains belonged to the hitherto-uncultured NOR5-4 and NOR5-12 subclades. Metabolic reconstructions revealed that the six strains likely have aerobic chemo- or photoheterotrophic lifestyles; five of them possess genes for proteorhodopsin or aerobic anoxygenic phototrophy. The presence of blue- or green-tuned proteorhodopsin in Halieaceae suggested their ability to adapt to light conditions varying with depth or coastal-to-open ocean transition. In addition to the genes of anaplerotic CO2 fixation, genes encoding a complete reductive glycine pathway for CO2 fixation were found in three strains. Putative polysaccharide utilization loci were detected in three strains, suggesting the association with phytoplankton blooms. Read mapping of various metagenomes and metatranscriptomes showed that the six strains are widely distributed and transcriptionally active in marine environments. Overall, the six strains genomically characterized in this study expand the phylogenetic and metabolic diversity of Halieaceae and likely serve as a culture resource for investigating the ecophysiological features of this environmentally relevant bacterial group. IMPORTANCE Although the family Halieaceae (OM60/NOR5 clade) is an abundant and cosmopolitan clade widely found in coastal seas and involved in interactions with phytoplankton, a limited number of cultured isolates are available. In this study, we isolated six pure cultured Halieaceae strains from coastal seawaters and performed a comparative physiological and genomic analysis to give insights into the phylogeny and metabolic potential of this family. The cultured strains exhibited diverse metabolic potential by harboring genes for anaplerotic CO2 fixation, proteorhodopsin, and aerobic anoxygenic phototrophy. Polysaccharide utilization loci detected in some of these strains also indicated an association with phytoplankton blooms. The cultivation of novel strains of Halieaceae and their genomic characteristics largely expanded the phylogenetic and metabolic diversity, which is important for future ecophysiological studies.}, }
@article {pmid36916558, year = {2023}, author = {Aditya, A and Tabashsum, Z and Alvarado Martinez, Z and Wei Tung, C and Suh, G and Nguyen, P and Biswas, D}, title = {Diarrheagenic Escherichia coli and Their Antibiotic Resistance Patterns in Dairy Farms and Their Microbial Ecosystems.}, journal = {Journal of food protection}, volume = {86}, number = {3}, pages = {100051}, doi = {10.1016/j.jfp.2023.100051}, pmid = {36916558}, issn = {1944-9097}, abstract = {Ruminants are the largest reservoir for all types of Escherichia coli, including the pathogenic ones, which can potentially be transmitted to humans via the food chain and environment. A longitudinal study was performed to estimate the prevalence and antibiotic-resistant pattern of pathogenic E. coli (pE.coli) strains in dairy farm environments. A total of 846 environmental samples (water, lagoon slurry, bedding, feed, feces, soil, and compost) were collected in summer over two years from five dairy farms in Maryland, USA. An additional 40 soil samples were collected in winter and summer seasons for evaluating microbiome composition. Collected environmental samples were screened for the presence of pE.coli, which was isolated using a selective culture medium, for later confirmation and virotyping using PCR with specific primers. The overall prevalence of pE.coli in dairy farms was 8.93% (71/846), with the most common virotype identified in isolates being ETEC, followed by STEC. The highest pE.coli prevalence were recorded in lagoon slurry (21.57%) while the lowest was in compost heap (2.99%). Among isolates, 95.87% of the virotypes were resistant to 9 classes of antibiotics whereas only 4.12% were sensitive. The highest proportion (68.04%) of resistance was found for quinolones (e.g., ciprofloxacin). The resulting metagenomic analysis at the phylum and genus levels of the grazing land soil suggests that climatic conditions actively influence the abundance of bacteria. Proteobacteria, which contains many Gram-negative foodborne pathogens (including pE.coli), was the most predominant phylum, accounting for 26.70% and 24.93% of soil bacteria in summer and winter, respectively. In addition to relative abundance, there was no significant difference in species diversity between seasons when calculated via Simpson (D) and Shannon (H) index. This study suggests that antibiotic-resistant E. coli virotypes are present in the dairy farm environment, and proper steps are warranted to control its transmission irrespective of seasonality.}, }
@article {pmid36916422, year = {2023}, author = {Wang, AJ and Song, D and Hong, YM and Liu, NN}, title = {Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the "microworld" age.}, journal = {Molecular omics}, volume = {}, number = {}, pages = {}, doi = {10.1039/d2mo00288d}, pmid = {36916422}, issn = {2515-4184}, abstract = {Colorectal cancer (CRC) is a multifactorial heterogeneous disease largely due to both genetic predisposition and environmental factors including the gut microbiota, a dynamic microbial ecosystem inhabiting the gastrointestinal tract. Elucidation of the molecular mechanisms by which the gut microbiota interacts with the host may contribute to the pathogenesis, diagnosis, and promotion of CRC. However, deciphering the influence of genetic variants and interactions with the gut microbial ecosystem is rather challenging. Despite recent advancements in single omics analysis, the application of multi-omics approaches to integrate multiple layers of information in the microbiome and host to introduce effective prevention, diagnosis, and treatment strategies is still in its infancy. Here, we integrate host- and microbe-based multi-omics studies, respectively, to provide a strategy to explore potential causal relationships between gut microbiota and colorectal cancer. Specifically, we summarize the recent multi-omics studies such as metagenomics combined with metabolomics and metagenomics combined with genomics. Meanwhile, the sample size and sample types commonly used in multi-omics research, as well as the methods of data analysis, were also generalized. We highlight multiple layers of information from multi-omics that need to be verified by different types of models. Together, this review provides new insights into the clinical diagnosis and treatment of colorectal cancer patients.}, }
@article {pmid36915639, year = {2023}, author = {Roslund, MI and Parajuli, A and Hui, N and Puhakka, R and Grönroos, M and Soininen, L and Nurminen, N and Oikarinen, S and Cinek, O and Kramná, L and Schroderus, AM and Laitinen, OH and Kinnunen, T and Hyöty, H and Sinkkonen, A}, title = {Skin, gut, and sand metagenomic data on placebo-controlled sandbox biodiversity intervention study.}, journal = {Data in brief}, volume = {47}, number = {}, pages = {109003}, pmid = {36915639}, issn = {2352-3409}, abstract = {The metagenomic data presented in this article are related to the published research of "A Placebo-controlled double-blinded test of the biodiversity hypothesis of immune-mediated diseases: Environmental microbial diversity elicits changes in cytokines and increase in T regulatory cells in young children" This database contains 16S ribosomal RNA (rRNA) metagenomics of sandbox sand and skin and gut microbiota of children in the intervention and placebo daycares. In intervention daycares, children aged 3-5 years were exposed to playground sand enriched with microbially diverse soil. In placebo daycares, children were exposed to visually similar as in intervention daycares, but microbially poor sand colored with peat. Sand, skin and gut metagenomics were analyzed at baseline and after 14 and 28 days of intervention by high throughput sequencing of bacterial 16S rRNA gene on the Illumina MiSeq platform. This dataset shows how skin bacterial community composition, including classes Gammaproteobacteria and Bacilli, changed, and how the relative abundance of over 30 bacterial genera shifted on the skin of children in the intervention treatment, while no shifts occurred in the placebo group.}, }
@article {pmid36915549, year = {2023}, author = {Qin, J and Ji, B and Ma, Y and Liu, X and Wang, T and Liu, G and Li, B and Wang, G and Gao, P}, title = {Diversity and potential function of pig gut DNA viruses.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e14020}, pmid = {36915549}, issn = {2405-8440}, abstract = {Viruses are ubiquitous in the gut of animals and play an important role in the ecology of the gut microbiome. The potential effects of these substances on the growth and development of the body are not fully known. Little is known about the effects of breeding environment on pig gut virome. Here, there are 3584 viral operational taxonomic units (vOTUs) longer than 5 kb identified by virus-enriched metagenome sequencing from 25 pig fecal samples. Only a small minority of vOTUs (11.16%) can be classified at the family level, and ∼50% of the genes could be annotated, supporting the concept of pig gut as reservoirs of substantial undescribed viral genetic diversity. The composition of pig gut virome in the six regions may be related to geography. There are only 20 viral clusters (VCs) shared among pig gut virome in six regions of Shanxi Province. These viruses rarely carry antibiotic resistance genes (ARGs). At the same time, they possess abundant auxiliary metabolic genes (AMGs) potentially involved in carbon, sulfur metabolism and cofactor biosynthesis, etc. This study has revealed the unique characteristics and potential function of pig gut DNA virome and established a foundation for the recognition of the viral roles in gut environment.}, }
@article {pmid36915411, year = {2023}, author = {Thippabhotla, S and Liu, B and Podgorny, A and Yooseph, S and Yang, Y and Zhang, J and Zhong, C}, title = {Integrated de novo gene prediction and peptide assembly of metagenomic sequencing data.}, journal = {NAR genomics and bioinformatics}, volume = {5}, number = {1}, pages = {lqad023}, pmid = {36915411}, issn = {2631-9268}, abstract = {Metagenomics is the study of all genomic content contained in given microbial communities. Metagenomic functional analysis aims to quantify protein families and reconstruct metabolic pathways from the metagenome. It plays a central role in understanding the interaction between the microbial community and its host or environment. De novo functional analysis, which allows the discovery of novel protein families, remains challenging for high-complexity communities. There are currently three main approaches for recovering novel genes or proteins: de novo nucleotide assembly, gene calling and peptide assembly. Unfortunately, their information dependency has been overlooked, and each has been formulated as an independent problem. In this work, we develop a sophisticated workflow called integrated Metagenomic Protein Predictor (iMPP), which leverages the information dependencies for better de novo functional analysis. iMPP contains three novel modules: a hybrid assembly graph generation module, a graph-based gene calling module, and a peptide assembly-based refinement module. iMPP significantly improved the existing gene calling sensitivity on unassembled metagenomic reads, achieving a 92-97% recall rate at a high precision level (>85%). iMPP further allowed for more sensitive and accurate peptide assembly, recovering more reference proteins and delivering more hypothetical protein sequences. The high performance of iMPP can provide a more comprehensive and unbiased view of the microbial communities under investigation. iMPP is freely available from https://github.com/Sirisha-t/iMPP.}, }
@article {pmid36915394, year = {2023}, author = {Dai, S and He, Q and Han, Z and Shen, W and Deng, Y and Wang, Y and Qiao, W and Yang, M and Zhang, Y}, title = {Uncovering the diverse hosts of tigecycline resistance gene tet(X4) in anaerobic digestion systems treating swine manure by epicPCR.}, journal = {Water research X}, volume = {19}, number = {}, pages = {100174}, pmid = {36915394}, issn = {2589-9147}, abstract = {The tet(X4) gene is a clinically important tigecycline resistance gene and has shown high persistence in livestock-related environments. However, the bacterial hosts of tet(X4) remain unknown due to the lack of appropriate approaches. Herein, a culture-independent and high-throughput epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction) method was developed, optimized, and demonstrated for the identification of bacterial hosts carrying tet(X4) from environmental samples. Considering the high sequence similarity between tet(X4) and other tet(X)-variant genes, specific primers and amplification conditions were screened and optimized to identify tet(X4) accurately and link tet(X4) with the 16S rRNA gene, which were further validated using artificially constructed bacterial communities. The epicPCR targeting tet(X4) was applied for the identification of bacterial hosts carrying this resistance gene in anaerobic digestion systems treating swine manure. A total of 19 genera were identified as tet(X4) hosts, which were distributed in the phyla Proteobacteria, Bacteroidota, Firmicutes, and Caldatribacteriota. Sixteen genera and two phyla that were identified have not been previously reported as tet(X4) bacterial hosts. The results indicated that a far more diverse range of bacteria was involved in harboring tet(X4) than previously realized. Compared with the tet(X4) hosts determined by correlation-based network analysis and metagenomic binning, epicPCR revealed a high diversity of tet(X4) hosts even at the phylum level. The epicPCR method developed in this study could be effectively employed to reveal the presence of tet(X4) bacterial hosts from a holistic viewpoint.}, }
@article {pmid36915382, year = {2023}, author = {Lo, EKK and Wang, X and Lee, PK and Wong, HC and Lee, JC and Gómez-Gallego, C and Zhao, D and El-Nezami, H and Li, J}, title = {Mechanistic insights into zearalenone-accelerated colorectal cancer in mice using integrative multi-omics approaches.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {1785-1796}, pmid = {36915382}, issn = {2001-0370}, abstract = {Zearalenone (ZEA), a secondary metabolite of Fusarium fungi found in cereal-based foods, promotes the growth of colon, breast, and prostate cancer cells in vitro. However, the lack of animal studies hinders a deeper mechanistic understanding of the cancer-promoting effects of ZEA. This study aimed to determine the effect of ZEA on colon cancer progression and its underlying mechanisms. Through integrative analyses of transcriptomics, metabolomics, metagenomics, and host phenotypes, we investigated the impact of a 4-week ZEA intervention on colorectal cancer in xenograft mice. Our results showed a twofold increase in tumor weight with the 4-week ZEA intervention. ZEA exposure significantly increased the mRNA and protein levels of BEST4, DGKB, and Ki67 and the phosphorylation levels of ERK1/2 and AKT. Serum metabolomic analysis revealed that the levels of amino acids, including histidine, arginine, citrulline, and glycine, decreased significantly in the ZEA group. Furthermore, ZEA lowered the alpha diversity of the gut microbiota and reduced the abundance of nine genera, including Tuzzerella and Rikenella. Further association analysis indicated that Tuzzerella was negatively associated with the expression of BEST4 and DGKB genes, serum uric acid levels, and tumor weight. Additionally, circulatory hippuric acid levels positively correlated with tumor weight and the expression of oncogenic genes, including ROBO3, JAK3, and BEST4. Altogether, our results indicated that ZEA promotes colon cancer progression by enhancing the BEST4/AKT/ERK1/2 pathway, lowering circulatory amino acid concentrations, altering gut microbiota composition, and suppressing short chain fatty acids production.}, }
@article {pmid36914646, year = {2023}, author = {Ngugi, DK and Acinas, SG and Sánchez, P and Gasol, JM and Agusti, S and Karl, DM and Duarte, CM}, title = {Abiotic selection of microbial genome size in the global ocean.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1384}, pmid = {36914646}, issn = {2041-1723}, abstract = {Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.}, }
@article {pmid36914318, year = {2023}, author = {Zhao, Y and Sun, C and Wang, S and Zhang, M and Li, Y and Xue, Q and Guo, Q and Lai, H}, title = {Widely targeted metabolomic, transcriptomic, and metagenomic profiling reveal microbe-plant-metabolic reprogramming patterns mediated by Streptomyces pactum Act12 enhance the fruit quality of Capsicum annuum L.}, journal = {Food research international (Ottawa, Ont.)}, volume = {166}, number = {}, pages = {112587}, doi = {10.1016/j.foodres.2023.112587}, pmid = {36914318}, issn = {1873-7145}, abstract = {Plant growth-promoting rhizobacteria, such as Streptomyces pactum Act12, promote crop growth and stress resistance, but their contribution to fruit quality is still poorly understood. Herein we conducted a field experiment to ascertain the effects of S. pactum Act12-mediated metabolic reprogramming and underlying mechanisms in pepper (Capsicum annuum L.) fruit based on widely targeted metabolomic and transcriptomic profiling. We additionally performed metagenomic analysis to elucidate the potential relationship between S. pactum Act12-mediated reshaping of rhizosphere microbial communities and pepper fruit quality. Soil inoculation with S. pactum Act12 considerably increased the accumulation of capsaicinoids, carbohydrates, organic acids, flavonoids, anthraquinones, unsaturated fatty acids, vitamins, and phenolic acids in pepper fruit samples. Consequently, fruit flavor, taste, and color were modified, accompanied by elevated contents of nutrients and bioactive compounds. Increased microbial diversity and recruitment of potentially beneficial taxa were observed in inoculated soil samples, with crosstalk between microbial gene functions and pepper fruit metabolism. The reformed structure and function of rhizosphere microbial communities were closely associated with pepper fruit quality. Our findings indicate that S. pactum Act12-mediated interactions between rhizosphere microbial communities and pepper plants are responsible for intricate fruit metabolic reprogramming patterns, which enhance not only overall fruit quality but also consumer acceptability.}, }
@article {pmid36913841, year = {2023}, author = {Vermote, L and De Roos, J and Cnockaert, M and Vandamme, P and Weckx, S and De Vuyst, L}, title = {New insights into the role of key microorganisms and wooden barrels during lambic beer fermentation and maturation.}, journal = {International journal of food microbiology}, volume = {394}, number = {}, pages = {110163}, doi = {10.1016/j.ijfoodmicro.2023.110163}, pmid = {36913841}, issn = {1879-3460}, abstract = {Belgian lambic beers are still produced through traditional craftsmanship. They rely on a spontaneous fermentation and maturation process that is entirely carried out in wooden barrels. The latter are used repetitively and may introduce some batch-to-batch variability. The present systematic and multiphasic study dealt with two parallel lambic beer productions carried out in nearly identical wooden barrels making use of the same cooled wort. It encompassed a microbiological and metabolomic approach. Further, a taxonomic classification and metagenome-assembled genome (MAG) investigation was based on shotgun metagenomics. These investigations provided new insights into the role of these wooden barrels and key microorganisms for this process. Indeed, besides their role in traditionality, the wooden barrels likely helped in establishing the stable microbial ecosystem of lambic beer fermentation and maturation by acting as an inoculation source of the necessary microorganisms, thereby minimizing batch-to-batch variations. They further provided a microaerobic environment, which aided in achieving the desirable succession of the different microbial communities for a successful lambic beer production process. Moreover, these conditions prevented excessive growth of acetic acid bacteria and, therefore, uncontrolled production of acetic acid and acetoin, which may lead to flavor deviations in lambic beer. Concerning the role of less studied key microorganisms for lambic beer production, it was shown that the Acetobacter lambici MAG contained several acid tolerance mechanisms toward the harsh environment of maturing lambic beer, whereas genes related to sucrose and maltose/maltooligosaccharide consumption and the glyoxylate shunt were absent. Further, a Pediococcus damnosus MAG possessed a gene encoding ferulic acid decarboxylase, possibly contributing to 4-vinyl compound production, as well as several genes, likely plasmid-based, related to hop resistance and biogenic amine production. Finally, contigs related to Dekkera bruxellensis and Brettanomyces custersianus did not possess genes involved in glycerol production, emphasizing the need for alternative external electron acceptors for redox balancing.}, }
@article {pmid36913533, year = {2023}, author = {Vilardi, K and Cotto, I and Bachmann, M and Parsons, M and Klaus, S and Wilson, C and Bott, CB and Pieper, KJ and Pinto, AJ}, title = {Co-Occurrence and Cooperation between Comammox and Anammox Bacteria in a Full-Scale Attached Growth Municipal Wastewater Treatment Process.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c09223}, pmid = {36913533}, issn = {1520-5851}, abstract = {Cooperation between comammox and anammox bacteria for nitrogen removal has been recently reported in laboratory-scale systems, including synthetic community constructs; however, there are no reports of full-scale municipal wastewater treatment systems with such cooperation. Here, we report intrinsic and extant kinetics as well as genome-resolved community characterization of a full-scale integrated fixed film activated sludge (IFAS) system where comammox and anammox bacteria co-occur and appear to drive nitrogen loss. Intrinsic batch kinetic assays indicated that majority of the aerobic ammonia oxidation was driven by comammox bacteria (1.75 ± 0.08 mg-N/g TS-h) in the attached growth phase, with minimal contribution by ammonia-oxidizing bacteria. Interestingly, a portion of total inorganic nitrogen (∼8%) was consistently lost during these aerobic assays. Aerobic nitrite oxidation assays eliminated the possibility of denitrification as a cause of nitrogen loss, while anaerobic ammonia oxidation assays resulted in rates consistent with anammox stoichiometry. Full-scale experiments at different dissolved oxygen (DO = 2 - 6 mg/L) setpoints indicated persistent nitrogen loss that was partly sensitive to DO concentrations. Genome-resolved metagenomics confirmed the high abundance (relative abundance 6.53 ± 0.34%) of two Brocadia-like anammox populations, while comammox bacteria within the Ca. Nitrospira nitrosa cluster were lower in abundance (0.37 ± 0.03%) and Nitrosomonas-like ammonia oxidizers were even lower (0.12 ± 0.02%). Collectively, our study reports for the first time the co-occurrence and cooperation of comammox and anammox bacteria in a full-scale municipal wastewater treatment system.}, }
@article {pmid36913445, year = {2023}, author = {Strobel, KM and Del Vecchio, G and Devaskar, SU and Calkins, KL}, title = {Gut Microbes and Circulating Cytokines in Preterm Infants with Growth Failure.}, journal = {The Journal of nutrition}, volume = {153}, number = {1}, pages = {120-130}, doi = {10.1016/j.tjnut.2022.10.005}, pmid = {36913445}, issn = {1541-6100}, abstract = {BACKGROUND: Growth failure (GF) is a multifactorial problem in preterm infants. The intestinal microbiome and inflammation may contribute to GF.<br><br>OBJECTIVES: This study's objective was to compare the gut microbiome and plasma cytokines in preterm infants with and without GF.<br><br>METHODS: This was a prospective cohort study of infants with birth weights of <1750 g. Infants with a weight or length z-score change from birth to discharge or death that was less than or equal to -0.8 (GF group) were compared with infants without GF [control (CON) group]. The primary outcome was the gut microbiome (at weeks 1-4 of age), assessed by 16S rRNA gene sequencing using Deseq2. Secondary outcomes included inferred metagenomic function and plasma cytokines. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States determined metagenomic function, which was compared using ANOVA. Cytokines were measured by 2-multiplexed immunometric assays and compared using Wilcoxon tests and linear mixed models.<br><br>RESULTS: GF (n = 14) and CON group (n = 13) had similar median (IQR) birth weight (1380 [780-1578] g vs. 1275 [1013-1580] g) and gestational age (29 [25-31] weeks vs. 30 [29-32] weeks). Compared with the CON group, the GF group had a greater abundance of Escherichia/Shigella in weeks 2 and 3, Staphylococcus in week 4, and Veillonella in weeks 3 and 4 (P-adjusted < 0.001 for all). Plasma cytokine concentrations did not differ significantly between the cohorts. When all time points are combined, fewer microbes were involved in TCA cycle activity in the GF group compared with the CON group (P = 0.023).<br><br>CONCLUSIONS: In this study, when compared with CON infants, GF infants had a distinct microbial signature with increased Escherichia/Shigella and Firmicutes and fewer microbes associated with energy production at later weeks of hospitalization. These findings may suggest a mechanism for aberrant growth.}, }
@article {pmid36913444, year = {2023}, author = {Larke, JA and Bacalzo, N and Castillo, JJ and Couture, G and Chen, Y and Xue, Z and Alkan, Z and Kable, ME and Lebrilla, CB and Stephensen, CB and Lemay, DG}, title = {Dietary Intake of Monosaccharides from Foods is Associated with Characteristics of the Gut Microbiota and Gastrointestinal Inflammation in Healthy US Adults.}, journal = {The Journal of nutrition}, volume = {153}, number = {1}, pages = {106-119}, doi = {10.1016/j.tjnut.2022.12.008}, pmid = {36913444}, issn = {1541-6100}, abstract = {BACKGROUND: Current assessment of dietary carbohydrates does not adequately reflect the nutritional properties and effects on gut microbial structure and function. Deeper characterization of food carbohydrate composition can serve to strengthen the link between diet and gastrointestinal health outcomes.<br><br>OBJECTIVES: The present study aims to characterize the monosaccharide composition of diets in a healthy US adult cohort and use these features to assess the relationship between monosaccharide intake, diet quality, characteristics of the gut microbiota, and gastrointestinal inflammation.<br><br>METHODS: This observational, cross-sectional study enrolled males and females across age (18-33 y, 34-49 y, and 50-65 y) and body mass index (normal, 18.5-24.99 kg/m[2]; overweight, 25-29.99 kg/m[2]; and obese, 30-44 kg/m[2]) categories. Recent dietary intake was assessed by the automated self-administered 24-h dietary recall system, and gut microbiota were assessed with shotgun metagenome sequencing. Dietary recalls were mapped to the Davis Food Glycopedia to estimate monosaccharide intake. Participants with >75% of carbohydrate intake mappable to the glycopedia were included (N = 180).<br><br>RESULTS: Diversity of monosaccharide intake was positively associated with the total Healthy Eating Index score (Pearson's r = 0.520, P = 1.2 &#xd7; 10[-13]) and negatively associated with fecal neopterin (Pearson's r = -0.247, P = 3.0 &#xd7; 10[-3]). Comparing high with low intake of specific monosaccharides revealed differentially abundant taxa (Wald test, P < 0.05), which was associated with the functional capacity to break down these monomers (Wilcoxon rank-sum test, P < 0.05).<br><br>CONCLUSIONS: Monosaccharide intake was associated with diet quality, gut microbial diversity, microbial metabolism, and gastrointestinal inflammation in healthy adults. As specific food sources were rich in particular monosaccharides, it may be possible in the future to tailor diets to fine-tune the gut microbiota and gastrointestinal function. This trial is registered at www.<br><br>CLINICALTRIALS: gov as NCT02367287.}, }
@article {pmid36912817, year = {2023}, author = {Wiegand, T and Wilkinson, R and Santiago-Frangos, A and Lynes, M and Hatzenpichler, R and Wiedenheft, B}, title = {Functional and Phylogenetic Diversity of Cas10 Proteins.}, journal = {The CRISPR journal}, volume = {}, number = {}, pages = {}, doi = {10.1089/crispr.2022.0085}, pmid = {36912817}, issn = {2573-1602}, abstract = {Cas10 proteins are large subunits of type III CRISPR RNA (crRNA)-guided surveillance complexes, many of which have nuclease and cyclase activities. Here, we use computational and phylogenetic methods to identify and analyze 2014 Cas10 sequences from genomic and metagenomic databases. Cas10 proteins cluster into five distinct clades that mirror previously established CRISPR-Cas subtypes. Most Cas10 proteins (85.0%) have conserved polymerase active-site motifs, while HD-nuclease domains are less well conserved (36.0%). We identify Cas10 variants that are split over multiple genes or genetically fused to nucleases activated by cyclic nucleotides (i.e., NucC) or components of toxin-antitoxin systems (i.e., AbiEii). To clarify the functional diversification of Cas10 proteins, we cloned, expressed, and purified five representatives from three phylogenetically distinct clades. None of the Cas10s are functional cyclases in isolation, and activity assays performed with polymerase domain active site mutants indicate that previously reported Cas10 DNA-polymerase activity may be a result of contamination. Collectively, this work helps clarify the phylogenetic and functional diversity of Cas10 proteins in type III CRISPR systems.}, }
@article {pmid36912756, year = {2023}, author = {Jiang, C and Wang, G and Zhang, J and Gu, S and Wang, X and Qin, W and Chen, K and Yuan, D and Chai, X and Yang, M and Zhou, F and Xiong, J and Miao, W}, title = {iGDP: an integrated Genome Decontamination Pipeline for wild ciliated microeukaryotes.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13782}, pmid = {36912756}, issn = {1755-0998}, abstract = {Ciliates are a large group of ubiquitous and highly diverse single-celled eukaryotes that play an essential role in the functioning of microbial food webs. However, their genomic diversity is far from clear due to the need to develop cultivation methods for most species, so most research is based on wild organisms that almost invariably contain contaminants. Here we establish an integrated Genome Decontamination Pipeline (iGDP) that combines homology search, telomere reads-assisted and clustering approaches to filter contaminated ciliate genome assemblies from wild specimens. We benchmarked the performance of iGDP using genomic data from a contaminated ciliate culture and the results showed that iGDP could recall 91.9% of the target sequences with 96.9% precision. We also used a synthetic dataset to offer guidelines for the application of iGDP in the removal of various groups of contaminants. Compared with several popular metagenome binning tools, iGDP could show better performance. To further validate the effectiveness of iGDP on real-world data, we applied it to decontaminate genome assemblies of three wild ciliate specimens and obtained their genomes with high quality comparable to that of previously well-studied model ciliate genomes. It is anticipated that the newly generated genomes and the established iGDP method will be valuable community resources for detailed studies on ciliate biodiversity, phylogeny, ecology and evolution. The pipeline (https://github.com/GWang2022/iGDP) can be implemented automatically to reduce manual filtering and classification and may be further developed to apply to other microeukaryotes.}, }
@article {pmid36912690, year = {2023}, author = {Shekarriz, E and Chen, J and Xu, Z and Liu, H}, title = {Disentangling the Functional Role of Fungi in Cold Seep Sediment.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0197822}, doi = {10.1128/spectrum.01978-22}, pmid = {36912690}, issn = {2165-0497}, abstract = {Cold seeps are biological oases of the deep sea fueled by methane, sulfates, nitrates, and other inorganic sources of energy. Chemolithoautotrophic bacteria and archaea dominate seep sediment, and their diversity and biogeochemical functions are well established. Fungi are likewise diverse, metabolically versatile, and known for their ability to capture and oxidize methane. Still, no study has ever explored the functional role of the mycobiota in the cold seep biome. To assess the complex role of fungi and fill in the gaps, we performed network analysis on 147 samples to disentangle fungal-prokaryotic interactions (fungal 18S and prokaryotic 16S) in the Haima cold seep region. We demonstrated that fungi are central species with high connectivity at the epicenter of prokaryotic networks, reduce their random-attack vulnerability by 60%, and enhance information transfer efficiency by 15%. We then scavenged a global metagenomic and metatranscriptomic data set from 10 cold seep regions for fungal genes of interest (hydrophobins, cytochrome P450s, and ligninolytic family of enzymes); this is the first study to report active transcription of 2,500+ fungal genes in the cold seep sediment. The genera Fusarium and Moniliella were of notable importance and directly correlated with high methane abundance in the sulfate-methane transition zone (SMTZ), likely due to their ability to degrade and solubilize methane and oils. Overall, our results highlight the essential yet overlooked contribution of fungi to cold seep biological networks and the role of fungi in regulating cold seep biogeochemistry. IMPORTANCE The challenges we face when analyzing eukaryotic metagenomic and metatranscriptomic data sets have hindered our understanding of cold seep fungi and microbial eukaryotes. This fact does not make the mycobiota any less critical in mediating cold seep biogeochemistry. On the contrary, many fungal genera can oxidize and solubilize methane, produce methane, and play a unique role in nutrient recycling via saprotrophic enzymatic activity. In this study, we used network analysis to uncover key fungal-prokaryotic interactions that can mediate methane biogeochemistry and metagenomics and metatranscriptomics to report that fungi are transcriptionally active in the cold seep sediment. With concerns over rising methane levels and cold seeps being a pivotal source of global methane input, our holistic understanding of methane biogeochemistry with all domains of life is essential. We ultimately encourage scientists to utilize state-of-the-art tools and multifaceted approaches to uncover the role of microeukaryotic organisms in understudied systems.}, }
@article {pmid36912656, year = {2023}, author = {Kao, S and Kao, CF and Chang, W and Ku, C}, title = {Widespread Distribution and Evolution of Poxviral Entry-Fusion Complex Proteins in Giant Viruses.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0494422}, doi = {10.1128/spectrum.04944-22}, pmid = {36912656}, issn = {2165-0497}, abstract = {Poxviruses are known to encode a set of proteins that form an entry-fusion complex (EFC) to mediate virus entry. However, the diversity, evolution, and origin of these EFC proteins remain poorly understood. Here, we identify the EFC protein homologs in poxviruses and other giant viruses of the phylum Nucleocytoviricota. The 11 EFC genes are present in almost all poxviruses, with the two smallest, G3 and O3, being absent in Entomopoxvirinae and basal lineages of Chordopoxvirinae. Five of the EFC genes are further grouped into two families, A16/G9/J5 and F9/L1, which are widely distributed across other major lineages of Nucleocytoviricota, including metagenome-assembled genomes, but are generally absent in viruses infecting algae or nonamoebozoan heterotrophic protists. The A16/G9/J5 and F9/L1 families cooccur, mostly as single copies, in 93% of the non-Poxviridae giant viruses that have at least one of them. Distribution and phylogenetic patterns suggest that both families originated in the ancestor of Nucleocytoviricota. In addition to the Poxviridae genes, homologs from each of the other Nucleocytoviricota families are largely clustered together, suggesting their ancient presence and vertical inheritance. Despite deep sequence divergences, we observed noticeable conservation of cysteine residues and predicted structures between EFC proteins of Poxviridae and other families. Overall, our study reveals widespread distribution of these EFC protein homologs beyond poxviruses, implies the existence of a conserved membrane fusion mechanism, and sheds light on host range and ancient evolution of Nucleocytoviricota. IMPORTANCE Fusion between virus and host membranes is critical for viruses to release genetic materials and to initiate infection. Whereas most viruses use a single protein for membrane fusion, poxviruses employ a multiprotein entry-fusion complex (EFC). We report that two major families of the EFC proteins are widely distributed within the virus phylum Nucleocytoviricota, which includes poxviruses and other double-stranded (dsDNA) giant viruses that infect animals, amoebozoans, algae, and various microbial eukaryotes. Each of these two protein families is structurally conserved, traces its origin to the root of Nucleocytoviricota, was passed down to the major subclades of Nucleocytoviricota, and is retained in most giant viruses known to infect animals and amoebozoans. The EFC proteins therefore represent a potential mechanism for virus entry in diverse giant viruses. We hypothesize that they may have facilitated the infection of an animal/amoebozoan-like host by the last Nucleocytoviricota common ancestor.}, }
@article {pmid36912626, year = {2023}, author = {Li, D and Ren, Z and Zhou, Y and Jiang, L and Zheng, M and Liu, G}, title = {Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0004723}, doi = {10.1128/aem.00047-23}, pmid = {36912626}, issn = {1098-5336}, abstract = {Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.}, }
@article {pmid36912232, year = {2023}, author = {Labourel, A and Parrou, JL and Deraison, C and Mercier-Bonin, M and Lajus, S and Potocki-Veronese, G}, title = {O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20220153}, pmid = {36912232}, issn = {1744-1358}, abstract = {Inflammatory bowel diseases (IBD) are modern diseases, with incidence rising around the world. They are associated with perturbation of the intestinal microbiota, and with alteration and crossing of the mucus barrier by the commensal bacteria that feed on it. In the process of mucus catabolism and invasion by gut bacteria, carbohydrate-active enzymes (CAZymes) play a critical role since mucus is mainly made up by O- and N-glycans. Moreover, the occurrence of IBD seems to be associated with low-fiber diets. Conversely, supplementation with oligosaccharides, such as human milk oligosaccharides (HMOs), which are structurally similar to intestinal mucins and could thus compete with them towards bacterial mucus-degrading CAZymes, has been suggested to prevent inflammation. In this mini-review, we will establish the current state of knowledge regarding the identification and characterization of mucus-degrading enzymes from both cultured and uncultured species of gut commensals and enteropathogens, with a particular focus on the present technological opportunities available to further the discovery of mucus-degrading CAZymes within the entire gut microbiome, by coupling microfluidics with metagenomics and culturomics. Finally, we will discuss the challenges to overcome to better assess how CAZymes targeting specific functional oligosaccharides could be involved in the modulation of the mucus-driven cross-talk between gut bacteria and their host in the context of IBD.}, }
@article {pmid36911308, year = {2023}, author = {Martinez, ND}, title = {Predicting ecosystem metaphenome from community metagenome: A grand challenge for environmental biology.}, journal = {Ecology and evolution}, volume = {13}, number = {3}, pages = {e9872}, pmid = {36911308}, issn = {2045-7758}, abstract = {Elucidating how an organism's characteristics emerge from its DNA sequence has been one of the great triumphs of biology. This triumph has cumulated in sophisticated computational models that successfully predict how an organism's detailed phenotype emerges from its specific genotype. Inspired by that effort's vision and empowered by its methodologies, a grand challenge is described here that aims to predict the biotic characteristics of an ecosystem, its metaphenome, from nucleic acid sequences of all the species in its community, its metagenome. Meeting this challenge would integrate rapidly advancing abilities of environmental nucleic acids (eDNA and eRNA) to identify organisms, their ecological interactions, and their evolutionary relationships with advances in mechanistic models of complex ecosystems. Addressing the challenge would help integrate ecology and evolutionary biology into a more unified and successfully predictive science that can better help describe and manage ecosystems and the services they provide to humanity.}, }
@article {pmid36910237, year = {2023}, author = {Zhang, C and Shi, X and Zhang, J and Zhang, Y and Wang, W}, title = {Dynamics of soil microbiome throughout the cultivation life cycle of morel (Morchella sextelata).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {979835}, pmid = {36910237}, issn = {1664-302X}, abstract = {Although Morchella sextelata (morel) is a well-known, edible, and medicinal fungus widely cultivated in China, the dynamics and roles of its soil microbiome during cultivation are unclear. Using rhizosphere soil samples collected throughout the M. sextelata cultivation life cycle, we conducted a high-throughput metagenomic sequencing analysis, with an emphasis on variations in soil microbial composition, characteristic biomarkers, and ecological functions. We found that microbial relative abundance, alpha diversity, and structure varied significantly among fungal growth stages. A total of 47 stage-associated biomarkers were identified through a linear discriminant analysis of effect size. In addition, horizontal comparison of soil microbiomes exhibiting successful and failed primordium formation further confirmed primordium-associated microbes with possible key roles in primordium formation. A microbial function analysis revealed that nutrient metabolism-related pathways were enriched during mycelium and fruiting body stages, whereas the signal transduction pathway was enriched during the primordium stage. This result indicates that diverse microbes are required at different growth stages of M. sextelata. Our research has revealed the dynamic scenario of the soil microbiome throughout the cultivation life cycle of M. sextelata. The high-resolution microbial profiles uncovered in the present study provide novel insights that should contribute to the improvement of morel cultivation using microbial inoculants.}, }
@article {pmid36910224, year = {2023}, author = {Coskun, &#xd6;K and Gomez-Saez, GV and Beren, M and Ozcan, D and Hosgormez, H and Einsiedl, F and Orsi, WD}, title = {Carbon metabolism and biogeography of candidate phylum "Candidatus Bipolaricaulota" in geothermal environments of Biga Peninsula, Turkey.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1063139}, pmid = {36910224}, issn = {1664-302X}, abstract = {Terrestrial hydrothermal springs and aquifers are excellent sites to study microbial biogeography because of their high physicochemical heterogeneity across relatively limited geographic regions. In this study, we performed 16S rRNA gene sequencing and metagenomic analyses of the microbial diversity of 11 different geothermal aquifers and springs across the tectonically active Biga Peninsula (Turkey). Across geothermal settings ranging in temperature from 43 to 79°C, one of the most highly represented groups in both 16S rRNA gene and metagenomic datasets was affiliated with the uncultivated phylum "Candidatus Bipolaricaulota" (former "Ca. Acetothermia" and OP1 division). The highest relative abundance of "Ca. Bipolaricaulota" was observed in a 68°C geothermal brine sediment, where it dominated the microbial community, representing 91% of all detectable 16S rRNA genes. Correlation analysis of "Ca. Bipolaricaulota" operational taxonomic units (OTUs) with physicochemical parameters indicated that salinity was the strongest environmental factor measured associated with the distribution of this novel group in geothermal fluids. Correspondingly, analysis of 23 metagenome-assembled genomes (MAGs) revealed two distinct groups of "Ca. Bipolaricaulota" MAGs based on the differences in carbon metabolism: one group encoding the bacterial Wood-Ljungdahl pathway (WLP) for H2 dependent CO2 fixation is selected for at lower salinities, and a second heterotrophic clade that lacks the WLP that was selected for under hypersaline conditions in the geothermal brine sediment. In conclusion, our results highlight that the biogeography of "Ca. Bipolaricaulota" taxa is strongly correlated with salinity in hydrothermal ecosystems, which coincides with key differences in carbon acquisition strategies. The exceptionally high relative abundance of apparently heterotrophic representatives of this novel candidate Phylum in geothermal brine sediment observed here may help to guide future enrichment experiments to obtain representatives in pure culture.}, }
@article {pmid36910183, year = {2023}, author = {Xi, M and Deyett, E and Stajich, JE and El-Kereamy, A and Roper, MC and Rolshausen, PE}, title = {Microbiome diversity, composition and assembly in a California citrus orchard.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1100590}, pmid = {36910183}, issn = {1664-302X}, abstract = {The citrus root and rhizosphere microbiomes have been relatively well described in the literature, especially in the context of Huanglonbing disease. Yet questions addressing the assembly of root microbial endophytes have remained unanswered. In the above ground tree tissues, leaves and stems have been the research focus point, while flush and flower microbiomes, two important tissues in the vegetative and reproductive cycles of the tree, are not well described. In this study, the fungal and bacterial taxa in five biocompartments (bulk soil, rhizosphere, root endosphere, flower and flush) of citrus trees grown in a single California orchard were profiled using an amplicon-based metagenomic Illumina sequencing approach. Trees with no observable signs of abiotic or biotic stresses were sampled for two consecutive years during the floral development phase. The rhizosphere was the most biodiverse compartment compared to bulk soil, root endosphere, flower and flush microbiomes. In addition, the belowground bacteriome was more diverse than the mycobiome. Microbial richness decreased significantly from the root exosphere to the endosphere and was overall low in the above ground tissues. Root endophytic microbial community composition shared strong similarities to the rhizosphere but also contained few taxa from above ground tissues. Our data indicated compartmentalization of the microbiome with distinct profiles between above and below ground microbial communities. However, several taxa were present across all compartments suggesting the existence of a core citrus microbiota. These findings highlight key microbial taxa that could be engineered as biopesticides and biofertilizers for citriculture.}, }
@article {pmid36910168, year = {2023}, author = {Hu, B and Wang, J and Li, Y and Ge, J and Pan, J and Li, G and He, Y and Zhong, H and Wang, B and Huang, Y and Han, S and Xing, Y and He, H}, title = {Gut microbiota facilitates adaptation of the plateau zokor (Myospalax baileyi) to the plateau living environment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1136845}, pmid = {36910168}, issn = {1664-302X}, abstract = {Gut microbiota not only helps the hosts to perform many key physiological functions such as food digestion, energy harvesting and immune regulation, but also influences host ecology and facilitates adaptation of the host to extreme environments. Plateau zokors epitomize successful physiological adaptation to their living environment in the face of the harsh environment characterized by low temperature, low pressure and hypoxia in the Tibetan plateau region and high concentrations of CO2 in their burrows. Therefore, here we used a metagenomic sequencing approach to explore how gut microbiota contributed to the adaptive evolution of the plateau zokor on the Qinghai-Tibet Plateau. Our metagenomic results show that the gut microbiota of plateau zokors on the Tibetan plateau is not only enriched in a large number of species related to energy metabolism and production of short-chain fatty acids (SCFAs), but also significantly enriched the KO terms that involve carbohydrate uptake pathways, which well address energy uptake in plateau zokors while also reducing inflammatory responses due to low pressure, hypoxia and high CO2 concentrations. There was also a significant enrichment of tripeptidyl-peptidase II (TPPII) associated with antigen processing, apoptosis, DNA damage repair and cell division, which may facilitate the immune response and tissue damage repair in plateau zokors under extreme conditions. These results suggest that these gut microbiota and their metabolites together contribute to the physiological adaptation of plateau zokors, providing new insights into the contribution of the microbiome to the evolution of mammalian adaptation.}, }
@article {pmid36910167, year = {2023}, author = {Zhao, J and Rodriguez, J and Martens-Habbena, W}, title = {Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1140487}, pmid = {36910167}, issn = {1664-302X}, abstract = {The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.}, }
@article {pmid36909846, year = {2022}, author = {Li, H and Zhang, L and Zhang, K and Huang, Y and Liu, Y and Lu, X and Liao, W and Liu, X and Zhang, Q and Pan, W}, title = {Gut microbiota associated with cryptococcal meningitis and dysbiosis caused by anti-fungal treatment.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1086239}, pmid = {36909846}, issn = {1664-302X}, abstract = {The gut microbiota is a dynamic and highly diverse microbial ecosystem that affects many aspects of the host's physiology. An improved understanding of the gut microbiota could lead to better strategies for the diagnosis and therapy of cryptococcal meningitis (CM), but the impact of Cryptococcus infection and anti-fungal treatment on the gut microbiota has rarely been studied. We characterized the diversity and composition of the gut microbiota in CM patients at diagnosis and healthy controls (HCs) using metagenomic sequencing and determined the effects of anti-fungal drugs. We found that CM patients had distinct bacterial and fungal compositions compared with HCs, with eight differentially abundant fungal and 72 differentially abundant bacterial species identified between the two groups. CM patients showed an increased abundance of Enterococcus avium, Leuconostoc mesenteroides, and Weissella cibaria, and a decreased abundance of Prevotella spp. compared with HCs. However, anti-fungal treatment only led to minor changes in the intestinal microbiota. Moreover, both positive and negative correlations existed in fungal, bacterial, and clinical indicators. Our study suggests that the Cryptococcus neoformans infection caused a distinct dysbiosis of the gut microbiota and contributes valuable information implying potential links between the CM and gut microbiota.}, }
@article {pmid36909733, year = {2023}, author = {Chang, L and Qiu, L and Lei, N and Zhou, J and Guo, R and Gao, F and Dong, S and Chen, M and Wu, F and Qin, B}, title = {Characterization of fecal microbiota in cervical cancer patients associated with tumor stage and prognosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1145950}, pmid = {36909733}, issn = {2235-2988}, abstract = {Cervical cancer (CC) is the fourth most frequent malignancy among women worldwide, and its prevention and treatment are evolving rapidly. The gut microbiota has been reported to play a crucial role both in the preservation of homeostasis and the development of cervical cancer. In this study, we collected fecal samples to investigate the microbial signatures in cervical cancer patients compared with healthy controls using 16S rRNA sequencing analysis and metagenomic next-generation sequencing (mNGS) testing. Our findings demonstrated a substantial difference in the gut microbiota composition of cervical cancer patients and healthy controls. The disease and stage were most significantly negatively correlated with Ruminococcus 2, which might be considered a potential clinically relevant biomarker. Functions of differential microbiomes were also analyzed, indicating significant differences in metabolisms and biosynthesis between the two groups. These findings demonstrate that patients with cervical cancer have certain species of gut microbiota that are exclusive to them and particular species have the potential to be used in the prognosis of cervical cancer.}, }
@article {pmid36909730, year = {2023}, author = {MacDonald, T and Dunn, KA and MacDonald, J and Langille, MGI and Van Limbergen, JE and Bielawski, JP and Kulkarni, K}, title = {The gastrointestinal antibiotic resistome in pediatric leukemia and lymphoma patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1102501}, pmid = {36909730}, issn = {2235-2988}, abstract = {INTRODUCTION: Most children with leukemia and lymphoma experience febrile neutropenia. These are treated with empiric antibiotics that include β-lactams and/or vancomycin. These are often administered for extended periods, and the effect on the resistome is unknown.<br><br>METHODS: We examined the impact of repeated courses and duration of antibiotic use on the resistome of 39 pediatric leukemia and lymphoma patients. Shotgun metagenome sequences from 127 stool samples of pediatric oncology patients were examined for abundance of antibiotic resistance genes (ARGs) in each sample. Abundances were grouped by repeated courses (no antibiotics, 1-2 courses, 3+ courses) and duration (no use, short duration, long and/or mixed durationg) of &#x3b2;-lactams, vancomycin and "any antibiotic" use. We assessed changes in both taxonomic composition and prevalence of ARGs among these groups.<br><br>RESULTS: We found that Bacteroidetes taxa and &#x3b2;-lactam resistance genes decreased, while opportunistic Firmicutes and Proteobacteria taxa, along with multidrug resistance genes, increased with repeated courses and/or duration of antibiotics. Efflux pump related genes predominated (92%) among the increased multidrug genes. While we found &#x3b2;-lactam ARGs present in the resistome, the taxa that appear to contain them were kept in check by antibiotic treatment. Multidrug ARGs, mostly efflux pumps or regulators of efflux pump genes, were associated with opportunistic pathogens, and both increased in the resistome with repeated antibiotic use and/or increased duration.<br><br>CONCLUSIONS: Given the strong association between opportunistic pathogens and multidrug-related efflux pumps, we suggest that drug efflux capacity might allow the opportunistic pathogens to persist or increase despite repeated courses and/or duration of antibiotics. While drug efflux is the most direct explanation, other mechanisms that enhance the ability of opportunistic pathogens to handle environmental stress, or other aspects of the treatment environment, could also contribute to their ability to flourish within the gut during treatment. Persistence of opportunistic pathogens in an already dysbiotic and weakened gastrointestinal tract could increase the likelihood of life-threatening blood borne infections. Of the 39 patients, 59% experienced at least one gastrointestinal or blood infection and 60% of bacteremia's were bacteria found in stool samples. Antimicrobial stewardship and appropriate use and duration of antibiotics could help reduce morbidity and mortality in this vulnerable population.}, }
@article {pmid36909719, year = {2023}, author = {Dai, J and Lian, X and Mo, J and Li, X and Mo, W and Wang, H and Jiang, J}, title = {Case report: A clinical case study of six patients with Chlamydia psittaci pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1084882}, pmid = {36909719}, issn = {2235-2988}, abstract = {OBJECTIVE: To investigate the clinical features, diagnosis, and treatment of Chlamydia psittaci (C. psittaci) pneumonia.<br><br>METHODS: We retrospectively analyzed the clinical data of six patients with C. psittaci pneumonia who were admitted to the Division of Pulmonary and Critical Care Medicine of the Second Hospital of Jiaxing from December 2021 to September 2022.<br><br>RESULTS: All patients reported a fever and other accompanying symptoms, including cough (5/6), chest tightness (1/6), fatigue (2/6), and headache (1/6). Laboratory results showed that all patients had high levels of C-reactive protein (CRP&#x2265;70 mg/L), procalcitonin (PCT; 2 patients with PCT levels &#x2265;0.5 ng/L), and erythrocyte sedimentation rate (ESR). Lactate dehydrogenase (LDH) and aspartate aminotransferase (AST) levels were elevated in 3/6 and of 2/6 patients, respectively. Chest computed tomography (CT) of most patients showed patchy, high-density shadows with partial consolidation, accompanied by air bronchogram signs and pleural effusion. Six patients were diagnosed with C. psittaci pneumonia using metagenomic next-generation sequencing (mNGS). They showed favorable outcomes following immediate adjustment of the regimen to doxycycline-based therapy and hydration, nutrition, and other follow-up treatments. In the imaging findings obtained at one-two month, the lesions were completely cleared, suggesting a favorable prognosis.<br><br>CONCLUSION: Patients with C. psittaci pneumonia commonly present sepsis and rapidly progressing disease. Early diagnosis is critical for C. psittaci pneumonia using mNGS, which can lead to favorable prognoses via immediate adjustment therapies.}, }
@article {pmid36909625, year = {2023}, author = {Verhoeve, VI and Lehman, SS and Driscoll, TP and Beckmann, JF and Gillespie, JJ}, title = {Metagenome diversity illuminates origins of pathogen effectors.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.02.26.530123}, pmid = {36909625}, abstract = {Recent metagenome assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. Discovery of basal lineages (Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles reveals an evolutionary timepoint for the transition to host dependency, which occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system (T4SS) and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for derived rickettsial pathogens. MAG analysis also substantially increased diversity for genus Rickettsia and delineated a basal lineage (Tisiphia) that stands to inform on the rise of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages indicates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, illuminating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role shaping the rvh effector landscape, as evinced by the discover of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can provide incredible insight on the origins of pathogen effectors and how their architectural modifications become tailored to eukaryotic host cell biology.}, }
@article {pmid36908773, year = {2023}, author = {Murray, AK and Zhang, L and Snape, J and Gaze, WH}, title = {Functional metagenomic libraries generated from anthropogenically impacted environments reveal importance of metabolic genes in biocide and antibiotic resistance.}, journal = {Current research in microbial sciences}, volume = {4}, number = {}, pages = {100184}, pmid = {36908773}, issn = {2666-5174}, abstract = {Anthropogenic activities result in the release of antimicrobial resistant bacteria and a cocktail of antimicrobial compounds into the environment that may directly select or indirectly co-select for antimicrobial resistance (AMR). Many studies use metagenome sequencing or qPCR-based approaches to study the environmental resistome but these methods are limited by a priori knowledge. In this study, a functional metagenomic approach was used to explore biocide resistance mechanisms in two contaminated environments and a pristine site, and to identify whether potentially novel genes conferring biocide resistance also conferred resistance or reduced susceptibility to antibiotics. Resistance was predominately mediated through novel mechanisms exclusive of the well-known qac efflux genes. UDP-galactose 4-epimerase (galE) -like genes were identified in both contaminated environments and were shown to confer cross-resistance to biocides and clinically important antibiotics for the first time (to our knowledge), compared to knockout mutants. GalE -like genes were also co-located with transposons, suggesting mobilisation potential. These results show that housekeeping genes may play a significant yet underappreciated role in AMR in environmental microbiomes.}, }
@article {pmid36908513, year = {2023}, author = {Ganda, E and Chakrabarti, A and Sardi, MI and Tench, M and Kozlowicz, BK and Norton, SA and Warren, LK and Khafipour, E}, title = {Saccharomyces cerevisiae fermentation product improves robustness of equine gut microbiome upon stress.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1134092}, pmid = {36908513}, issn = {2297-1769}, abstract = {INTRODUCTION: Nutritional and environmental stressors can disturb the gut microbiome of horses which may ultimately decrease their health and performance. We hypothesized that supplementation with a yeast-derived postbiotic (Saccharomyces cerevisiae fermentation product-SCFP) would benefit horses undergoing an established model of stress due to prolonged transportation.<br><br>METHODS: Quarter horses (n = 20) were blocked based on sex, age (22 &#xb1; 3 mo) and body weight (439 &#xb1; 3 kg) and randomized to receive either a basal diet of 60% hay and 40% concentrate (CON) or the basal diet supplemented with 21 g/d Diamond V TruEquine C (SCFP; Diamond V, Cedar Rapids, IA) for 60 days. On day 57, horses were tethered with their heads elevated 35cm above wither height for 12 h to induce mild upper respiratory tract inflammation. Fecal samples were collected at days 0, 28, and 56 before induction of stress, and at 0, 12, 24, and 72 h post-stress and subjected to DNA extraction and Nanopore shotgun metagenomics. Within sample (alpha) diversity was evaluated by fitting a linear model and between sample (beta) diversity was tested with permutational ANOVA.<br><br>RESULTS: The SCFP stabilized alpha diversity across all time points, whereas CON horses had more fluctuation (P < 0.05) at 12, 24, and 72 h post-challenge compared to d 56. A significant difference between CON and SCFP was observed at 0 and 12 h. There was no difference in beta-diversity between SCFP and CON on d 56.<br><br>DISCUSSION: Taken together, these observations led us to conclude that treatment with SCFP resulted in more robust and stable microbial profiles in horses after stress challenge.}, }
@article {pmid36908366, year = {2023}, author = {Pradhan, S and Prabhakar, MR and Karthika Parvathy, KR and Dey, B and Jayaraman, S and Behera, B and Paramasivan, B}, title = {Metagenomic and physicochemical analysis of Kombucha beverage produced from tea waste.}, journal = {Journal of food science and technology}, volume = {60}, number = {3}, pages = {1088-1096}, pmid = {36908366}, issn = {0022-1155}, abstract = {UNLABELLED: Kombucha beverage produced through fermentation of sugared tea using bacteria and yeast has gained attention for its beneficial health benefits. However, the cost linked to the raw materials often increases the upstream process expenses, thereby the overall operating expenditures. Thus, there is a need to explore alternative waste and cost-effective raw materials for Kombucha fermentation. The present study, compared the physico-chemical and microbial growth pattern of Kombucha beverage production using tea waste from the tea processing industries with that of the green/black tea, reporting similar trends irrespective of its type. Further, the amplicon sequencing of 16S rRNA showed dominant presence of Komagataeibacter rhaeticus and high throughput sequencing of ITS1 confirmed the presence of yeast species similar to Brettanomyces bruxellensis in the tea waste based Kombucha beverage. Appreciable amount of carbohydrates (8.5/100 g) and energy (34 kcal/100 g) with appropriate organoleptic properties favourable for human consumption were also observed during the nutritional content and qualitative property assessment. The overall study showed a broad taxonomic and functional diversity existing during Kombucha fermentation process with tea waste to maintain a sustained eco-system to facilitate cost-effective beverage production with desired properties for safe consumption.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-022-05476-3.}, }
@article {pmid36908212, year = {2023}, author = {Wu, Q and Wu, Y and Zhao, Y and Zhang, Y and Cao, J and Wu, D and Zhou, J and Chen, F}, title = {Adenovirus infection diagnosed by metagenomic next-generation sequencing after haploidentical hematopoietic stem cell transplantation: A multicenter study in China.}, journal = {Transplant infectious disease : an official journal of the Transplantation Society}, volume = {}, number = {}, pages = {e14054}, doi = {10.1111/tid.14054}, pmid = {36908212}, issn = {1399-3062}, abstract = {OBJECTIVE: This study aims to observe and analyze the clinical characteristics and prognosis of adenovirus (ADV) infection diagnosed by metagenomic next-generation sequencing (mNGS) after haploidentical hematopoietic stem cell transplantation (Haplo-HSCT), which was performed following Beijing Protocol.<br><br>METHODS: The clinical data of patients who developed ADV infection diagnosed by mNGS after Haplo-HSCT between January 2019 and March 2021, recorded in three transplantation centers, were retrospectively analyzed. Potential risk factors for infection and the clinical manifestations of ADV involvement in different end-organs were also studied. Additionally, the patient prognosis regarding the available treatment was observed.<br><br>RESULTS: A total of seven patients were diagnosed with ADV infection by the mNGS technique after Haplo-HSCT of 976 patients enrolled. The risk factors for infection included antithymocyte globulin steroid-refractory graft-versus-host disease (GVHD) history, CD25 monoclonal antibody or ruxolitinib treatment history and <300 cells/&#x3bc;L of CD3+ T cells count in peripheral blood. The clinical manifestations of ADV infection included encephalitis, hepatitis, cystitis, and pneumonia. Six patients were treated with cidofovir (CDV) and intravenous immunoglobulin (IVIg), and one with CDV, ribavirin, IVIg, thymosin Alpha-1 for injection and low-dose donor lymphocyte infusion. One case showed negative ADV DNA results with improved conditions; however, the patient died of the relapse of the primary disease in the later stage. The remaining six died of ADV infection.<br><br>CONCLUSION: mNGS can provide screening for ADV and information on ADV subtypes, helpful to understand tissue tropism. This technique could be useful in diagnosing patients at high risk for ADV infection. ADV infection can involve multiple organs, has difficulty in early diagnosis, and has a poor prognosis. Currently, effective treatments are inadequate.}, }
@article {pmid36907988, year = {2023}, author = {Mannion, A and Sheh, A and Shen, Z and Dzink-Fox, J and Piazuelo, MB and Wilson, KT and Peek, R and Fox, JG}, title = {Shotgun Metagenomics of Gastric Biopsies Reveals Compositional and Functional Microbiome Shifts in High- and Low-Gastric-Cancer-Risk Populations from Colombia, South America.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2186677}, doi = {10.1080/19490976.2023.2186677}, pmid = {36907988}, issn = {1949-0984}, abstract = {Along with Helicobacter pylori infection, the gastric microbiota is hypothesized to modulate stomach cancer risk in susceptible individuals. Whole metagenomic shotgun sequencing (WMS) is a sequencing approach to characterize the microbiome with advantages over traditional culture and 16S rRNA sequencing including identification of bacterial and non-bacterial taxa, species/strain resolution, and functional characterization of the microbiota. In this study, we used WMS to survey the microbiome in extracted DNA from antral gastric biopsy samples from Colombian patients residing in the high-risk gastric cancer town Túquerres (n = 10, H. pylori-positive = 7) and low-risk town of Tumaco (n = 10, H. pylori-positive = 6). Kraken2/Bracken was used for taxonomic classification and abundance. Functional gene profiles were inferred by InterProScan and KEGG analysis of assembled contigs and gene annotation. The most abundant taxa represented bacteria, non-human eukaryota, and viral genera found in skin, oral, food, and plant/soil environments including Staphylococus, Streptococcus, Bacillus, Aspergillus, and Siphoviridae. H. pylori was the predominant taxa present in H. pylori-positive samples. Beta diversity was significantly different based on H. pylori-status, risk group, and sex. WMS detected more bacterial taxa than 16S rRNA sequencing and aerobic, anaerobic, and microaerobic culture performed on the same gastric biopsy samples. WMS identified significant differences in functional profiles found between H. pylori-status, but not risk or sex groups. H. pylori-positive samples were significantly enriched for H. pylori-specific genes including virulence factors such as vacA, cagA, and urease, while carbohydrate and amino acid metabolism genes were enriched in H. pylori-negative samples. This study shows WMS has the potential to characterize the taxonomy and function of the gastric microbiome as risk factors for H. pylori-associated gastric disease. Future studies will be needed to compare and validate WMS versus traditional culture and 16S rRNA sequencing approaches for characterization of the gastric microbiome.}, }
@article {pmid36906632, year = {2023}, author = {Xiao, Y and Wang, H and Lan, Y and Zhong, C and Yan, G and Xu, Z and Lu, G and Chen, J and Wei, T and Wong, WC and Kwan, YH and Qian, PY}, title = {Changes in community structures and functions of the gut microbiomes of deep-sea cold seep mussels during in situ transplantation experiment.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {17}, pmid = {36906632}, issn = {2524-4671}, abstract = {BACKGROUND: Many deep-sea invertebrates largely depend on chemoautotrophic symbionts for energy and nutrition, and some of them have reduced functional digestive tracts. By contrast, deep-sea mussels have a complete digestive system although symbionts in their gills play vital roles in nutrient supply. This digestive system remains functional and can utilise available resources, but the roles and associations among gut microbiomes in these mussels remain unknown. Specifically, how the gut microbiome reacts to environmental change is unclear.<br><br>RESULTS: The meta-pathway analysis showed the nutritional and metabolic roles of the deep-sea mussel gut microbiome. Comparative analyses of the gut microbiomes of original and transplanted mussels subjected to environmental change revealed shifts in bacterial communities. Gammaproteobacteria were enriched, whereas Bacteroidetes were slightly depleted. The functional response for the shifted communities was attributed to the acquisition of carbon sources and adjusting the utilisation of ammonia and sulphide. Self-protection was observed after transplantation.<br><br>CONCLUSION: This study provides the first metagenomic insights into the community structure and function of the gut microbiome in deep-sea chemosymbiotic mussels and their critical mechanisms for adapting to changing environments and meeting of essential nutrient demand.}, }
@article {pmid36906612, year = {2023}, author = {Neumann, CJ and Mahnert, A and Kumpitsch, C and Kiu, R and Dalby, MJ and Kujawska, M and Madl, T and Kurath-Koller, S and Urlesberger, B and Resch, B and Hall, LJ and Moissl-Eichinger, C}, title = {Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1349}, pmid = {36906612}, issn = {2041-1723}, abstract = {Preterm infants with very low birthweight are at serious risk for necrotizing enterocolitis. To functionally analyse the principles of three successful preventive NEC regimens, we characterize fecal samples of 55 infants (<1500 g, n = 383, female = 22) longitudinally (two weeks) with respect to gut microbiome profiles (bacteria, archaea, fungi, viruses; targeted 16S rRNA gene sequencing and shotgun metagenomics), microbial function, virulence factors, antibiotic resistances and metabolic profiles, including human milk oligosaccharides (HMOs) and short-chain fatty acids (German Registry of Clinical Trials, No.: DRKS00009290). Regimens including probiotic Bifidobacterium longum subsp. infantis NCDO 2203 supplementation affect microbiome development globally, pointing toward the genomic potential to convert HMOs. Engraftment of NCDO 2203 is associated with a substantial reduction of microbiome-associated antibiotic resistance as compared to regimens using probiotic Lactobacillus rhamnosus LCR 35 or no supplementation. Crucially, the beneficial effects of Bifidobacterium longum subsp. infantis NCDO 2203 supplementation depends on simultaneous feeding with HMOs. We demonstrate that preventive regimens have the highest impact on development and maturation of the gastrointestinal microbiome, enabling the establishment of a resilient microbial ecosystem that reduces pathogenic threats in at-risk preterm infants.}, }
@article {pmid36906058, year = {2023}, author = {Zhou, Y and Wang, Y and Yang, L and Kong, Q and Zhang, H}, title = {Microbial degradation mechanisms of surface petroleum contaminated seawater in a typical oil trading port.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {324}, number = {}, pages = {121420}, doi = {10.1016/j.envpol.2023.121420}, pmid = {36906058}, issn = {1873-6424}, abstract = {Petroleum hydrocarbons are significant new persistent organic pollutants for marine oil spill risk areas. Oil trading ports, in turn, have become major bearers of the risk of offshore oil pollution. However, studies on the molecular mechanisms of microbial degradation of petroleum pollutants by natural seawater are limited. Here, an in situ microcosm study was conducted. Combined with metagenomics, differences in metabolic pathways and in the gene abundances of total petroleum hydrocarbons (TPH) are revealed under different conditions. About 88% degradation of TPH was shown after 3 weeks of treatment. The positive responders to TPH were concentrated in the genera Cycloclasticus, Marivita and Sulfitobacter of the orders Rhodobacterales and Thiotrichales. The genera Marivita, Roseobacter, Lentibacter and Glaciecola were key degradation species when mixing dispersants with oil, and all of the above are from the Proteobacteria phylum. The analysis showed that the biodegradability of aromatic compounds, polycyclic aromatic hydrocarbon and dioxin were enhanced after the oil spill, and genes with higher abundances of bphAa, bsdC, nahB, doxE and mhpD were found, but the photosynthesis-related mechanism was inhibited. The dispersant treatment effectively stimulated the microbial degradation of TPH and then accelerated the succession of microbial communities. Meanwhile, functions such as bacterial chemotaxis and carbon metabolism (cheA, fadeJ and fadE) were better developed, but the degradation of persistent organic pollutants such as polycyclic aromatic hydrocarbons was weakened. Our study provides insights into the metabolic pathways and specific functional genes for oil degradation by marine microorganisms and will help improve the application and practice of bioremediation.}, }
@article {pmid36905873, year = {2023}, author = {Vandamme, P and Peeters, C and Hettiarachchi, A and Cnockaert, M and Carlier, A}, title = {Govania unica gen. nov., sp. nov., a rare biosphere bacterium that represents a novel family in the class Alphaproteobacteria.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {3}, pages = {126405}, doi = {10.1016/j.syapm.2023.126405}, pmid = {36905873}, issn = {1618-0984}, abstract = {Strain LMG 31809 [T] was isolated from a top soil sample of a temperate, mixed deciduous forest in Belgium. Comparison of its 16S rRNA gene sequence with that of type strains of bacteria with validly published names positioned it in the class Alphaproteobacteria and highlighted a major evolutionary divergence from its near neighbor species which represented species of the orders Emcibacterales and Sphingomonadales. 16S rRNA amplicon sequencing of the same soil sample revealed a highly diverse community in which Acidobacteria and Alphaproteobacteria predominated, but failed to yield amplicon sequence variants highly similar to that of strain LMG 31809 [T]. There were no metagenome assembled genomes that corresponded to the same species and a comprehensive analysis of public 16S rRNA amplicon sequencing data sets demonstrated that strain LMG 31809 [T] represents a rare biosphere bacterium that occurs at very low abundances in multiple soil and water-related ecosystems. The genome analysis suggested that this strain is a strictly aerobic heterotroph that is asaccharolytic and uses organic acids and possibly aromatic compounds as growth substrates. We propose to classify LMG 31809 [T] as a novel species within a novel genus, Govania unica gen. nov., sp. nov, within the novel family Govaniaceae of the class Alphaproteobacteria. Its type strain is LMG 31809 [T] (=CECT 30155 [T]). The whole-genome sequence of strain LMG 31809 [T] has a size of 3.21 Mbp. The G + C content is 58.99 mol%. The 16S rRNA gene and whole-genome sequences of strain LMG 31809 [T] are publicly available under accession numbers OQ161091 and JANWOI000000000, respectively.}, }
@article {pmid36602781, year = {2023}, author = {Pichardo, PFA and Hellums, RN and Hao, J and Savatt, JM and Hassen, D and Pellitteri, PK and Alvi, M and Buchanan, AH and Purdy, NC}, title = {Thyroidectomy Outcomes in Patients Identified With RET Pathogenic Variants Through a Population Genomic Screening Program.}, journal = {JAMA otolaryngology-- head &amp; neck surgery}, volume = {149}, number = {3}, pages = {195-202}, pmid = {36602781}, issn = {2168-619X}, mesh = {Male ; Humans ; Female ; Middle Aged ; Thyroidectomy/methods ; *Carcinoma, Medullary/genetics/pathology/surgery ; Retrospective Studies ; Cross-Sectional Studies ; Metagenomics ; Proto-Oncogene Proteins c-ret/genetics ; Proto-Oncogene Mas ; *Thyroid Neoplasms/diagnosis/genetics/surgery ; Genetic Testing ; }, abstract = {IMPORTANCE: Population-based genomic screening can facilitate early detection of medullary thyroid carcinoma (MTC) in patients with pathogenic/likely pathogenic (P/LP) RET variants.<br><br>OBJECTIVE: To evaluate the clinical treatment and patient outcomes after identification of P/LP RET proto-oncogene variants associated with the risk of MTC via a population genomic screening program.<br><br>DESIGN, SETTING, PARTICIPANTS: This retrospective cross-sectional study was completed between June 1, 2016, and May 31, 2022, for a mean follow-up period of 22.4 months (range, 2-76 months). The study included patients who were identified as having P/LP RET variants through a population genomic screening program at a rural tertiary care center and who underwent thyroidectomy after results disclosure.<br><br>MAIN OUTCOMES AND MEASURES: The outcomes of interest were preoperative evaluation and treatment-related outcomes. Measures included imaging and laboratory findings, extent of surgery, pathologic diagnosis, and staging.<br><br>RESULTS: Seventy-five patients were identified as having P/LP RET variants exclusively through genomic screening. Twenty of these patients (27%; 11 women [55%] and 9 men [45%]; median age, 48 years [range, 22-73 years]) underwent total thyroidectomy; 13 of these patients (65%) also had a central neck dissection. No patients had clinically apparent disease at the time of surgery. Pathologic findings indicated MTC for 12 patients and papillary thyroid carcinoma in 2. Of patients with MTC, 10 had stage I disease, 1 had stage II disease, 1 had stage III disease, and none had stage IV disease. Based on postoperative surveillance imaging and laboratory results, no patient had evidence of recalcitrant disease.<br><br>CONCLUSIONS AND RELEVANCE: In this cross-sectional study, all malignant neoplasms identified on surgical pathology were clinically occult, with surgical intervention based solely on the identification of the P/LP RET variant via population genomic screening. This finding suggests that genomic screening may provide opportunities for early detection and treatment of MTC, with the potential for improved patient outcomes.}, }
@article {pmid36910129, year = {2022}, author = {Ericsson, AC and Bains, M and McAdams, Z and Daniels, J and Busi, SB and Waschek, JA and Dorsam, GP}, title = {The G Protein-Coupled Receptor, VPAC1, Mediates Vasoactive Intestinal Peptide-Dependent Functional Homeostasis of the Gut Microbiota.}, journal = {Gastro hep advances}, volume = {1}, number = {2}, pages = {253-264}, pmid = {36910129}, issn = {2772-5723}, abstract = {BACKGROUND AND AIMS: Vasoactive intestinal peptide (VIP) is a neuropeptide involved in the regulation of feeding behavior and circadian rhythms, metabolism, and immunity. Previous studies revealed the homeostatic effects of VIP signaling on the gut microbiota. VIP-deficient mice demonstrate a gut microbiota dysbiosis characterized by reduced α-diversity and decreased relative abundance (RA) of Gram-positive Firmicutes. However, the mechanism by which VIP signaling affects changes in the microbiota is unknown.<br><br>METHODS: To investigate the role of the 2 cognate G protein-coupled receptors for VIP (VPAC1 and VPAC2) in VIP-mediated homeostasis of the microbiota, fecal samples from VPAC1- and VPAC2-deficient, heterozygous, and wild-type littermate mice were assessed via targeted amplicon sequencing. Their microbiota profiles were additionally compared with microbiota from VIP-deficient, heterozygous, and wild-type littermates, where genotype-dependent changes in the composition and predicted function of each cohort were compared.<br><br>RESULTS: While wild-type mice in each line differed in &#x3b1;-diversity and &#x3b2;-diversity, consistent changes in both metrics were observed in VIP-deficient and VPAC1-deficient mice. This includes a dramatic reduction in &#x3b1;-diversity, increased RA of Proteobacteria and Bacteroidetes, and decreased RA of Lachnospiraceae, Ruminococcaceae, Muribaculaceae, and Rikenellaceae. Specific amplicon sequence variants and predicted functions found to differ significantly based on VIP or VPAC1 genotype were concordant in their directions of change. Multiplatform predicted functional profiling suggested a defective VIP-VPAC1 axis was associated with reduced amino acid degradation along with reduced quinol and quinone biosynthesis. Furthermore, alterations in predicted functions include increased sugar degradation, nitrate reduction, and fatty acid biosynthetic pathways, among other changes.<br><br>CONCLUSION: We conclude that VIP signaling through VPAC1 is critical for the maintenance of normal function of the gut microbiota.}, }
@article {pmid36904265, year = {2023}, author = {Wang, Z and Xu, X and Deji, Y and Gao, S and Wu, C and Song, Q and Shi, Z and Xiang, X and Zang, J and Su, J}, title = {Bifidobacterium as a Potential Biomarker of Sarcopenia in Elderly Women.}, journal = {Nutrients}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/nu15051266}, pmid = {36904265}, issn = {2072-6643}, abstract = {Gut microbial dysbiosis influences the development of sarcopenia. This case-control study explored the gut microbiota composition in elderly Chinese women with sarcopenia. The information from 50 cases and 50 controls was collected. Grip strength, body weight, body mass index, skeletal muscle mass, energy intake, and total and high-quality protein intake were lower in cases than in controls (p < 0.05). Gut microbiota metagenomic sequencing showed that phylum Bacteroides was significantly reduced in the case group, whereas genus Prevotella was more abundant (p < 0.05). Linear discriminant analysis (LDA) effect size showed that 9 and 13 distinct microbial taxa were enriched in the case and control groups, respectively (LDA > 2, p < 0.05), among which Prevotella copri and Bifidobacterium longum were significantly different (LDA > 4, p < 0.05). The AUC of Bifidobacterium longum was 0.674 (95% CI: 0.539-0.756). Elderly women with sarcopenia exhibited significantly different gut microbiota compositions than healthy controls.}, }
@article {pmid36902625, year = {2023}, author = {Mei, J and Hu, H and Zhu, S and Ding, H and Huang, Z and Li, W and Yang, B and Zhang, W and Fang, X}, title = {Diagnostic Role of mNGS in Polymicrobial Periprosthetic Joint Infection.}, journal = {Journal of clinical medicine}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/jcm12051838}, pmid = {36902625}, issn = {2077-0383}, abstract = {OBJECTIVES: The purpose of this study was to explore the clinical value of metagenomic next-generation sequencing (mNGS) in the diagnosis of polymicrobial periprosthetic joint infection (PJI).<br><br>METHODS: Patients with complete data who underwent surgery at our hospital between July 2017 and January 2021 for suspected periprosthetic joint infection (PJI), according to the 2018 ICE diagnostic criteria, were enrolled, and all patients underwent microbial culture and mNGS detection, which were performed on the BGISEQ-500 platform. Microbial cultures were performed on two samples of synovial fluid, six samples of tissue, and two samples of prosthetic sonicate fluid for each patient. The mNGS was performed on 10 tissues, 64 synovial fluid samples, and 17 prosthetic sonicate fluid samples. The results of mNGS testing were based on the interpretation of mNGS results in the previous literature and the assertions of microbiologists and orthopedic surgeons. The diagnostic efficacy of mNGS in polymicrobial PJI was assessed by comparing the results of conventional microbial cultures and mNGS.<br><br>RESULTS: A total of 91 patients were finally enrolled in this study. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of PJI were 71.0%, 95.4%, and 76.9%, respectively. The sensitivity, specificity, and accuracy of mNGS for the diagnosis of PJI were 91.3%, 86.3%, and 90.1%, respectively. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of polymicrobial PJI were 57.1%, 100%, and 91.3%, respectively. mNGS had a sensitivity, specificity, and accuracy of 85.7%, 60.0%, and 65.2%, respectively, for the diagnosis of polymicrobial PJI.<br><br>CONCLUSIONS: mNGS can improve the diagnosis efficiency of polymicrobial PJI, and the combination of culture and mNGS is a promising method to diagnose polymicrobial PJI.}, }
@article {pmid36902401, year = {2023}, author = {Rodríguez-Díaz, C and Martín-Reyes, F and Taminiau, B and Ho-Plágaro, A and Camargo, R and Fernandez-Garcia, F and Pinazo-Bandera, J and Toro-Ortiz, JP and Gonzalo, M and López-Gómez, C and Rodríguez-Pacheco, F and Rodríguez de Los Ríos, D and Daube, G and Alcain-Martinez, G and García-Fuentes, E}, title = {The Metagenomic Composition and Effects of Fecal-Microbe-Derived Extracellular Vesicles on Intestinal Permeability Depend on the Patient's Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, doi = {10.3390/ijms24054971}, pmid = {36902401}, issn = {1422-0067}, abstract = {The composition and impact of fecal-microbe-derived extracellular vesicles (EVs) present in different diseases has not been analyzed. We determined the metagenomic profiling of feces and fecal-microbe-derived EVs from healthy subjects and patients with different diseases (diarrhea, morbid obesity and Crohn's disease (CD)) and the effect of these fecal EVs on the cellular permeability of Caco-2 cells. The control group presented higher proportions of Pseudomonas and Rikenellaceae_RC9_gut_group and lower proportions of Phascolarctobacterium, Veillonella and Veillonellaceae_ge in EVs when compared with the feces from which these EVs were isolated. In contrast, there were significant differences in 20 genera between the feces and EV compositions in the disease groups. Bacteroidales and Pseudomonas were increased, and Faecalibacterium, Ruminococcus, Clostridium and Subdoligranum were decreased in EVs from control patients compared with the other three groups of patients. Tyzzerella, Verrucomicrobiaceae, Candidatus_Paracaedibacter and Akkermansia were increased in EVs from the CD group compared with the morbid obesity and diarrhea groups. Fecal EVs from the morbid obesity, CD and, mainly, diarrhea induced a significant increase in the permeability of Caco-2 cells. In conclusion, the metagenomic composition of fecal-microbe-derived EVs changes depending on the disease of the patients. The modification of the permeability of Caco-2 cells produced by fecal EVs depends on the disease of the patients.}, }
@article {pmid36902349, year = {2023}, author = {Melo, NCO and Cuevas-Sierra, A and Fernández-Cruz, E and de la O, V and Martínez, JA}, title = {Fecal Microbiota Composition as a Metagenomic Biomarker of Dietary Intake.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, doi = {10.3390/ijms24054918}, pmid = {36902349}, issn = {1422-0067}, abstract = {Gut microbiota encompasses the set of microorganisms that colonize the gastrointestinal tract with mutual relationships that are key for host homeostasis. Increasing evidence supports cross intercommunication between the intestinal microbiome and the eubiosis-dysbiosis binomial, indicating a networking role of gut bacteria as potential metabolic health surrogate markers. The abundance and diversity of the fecal microbial community are already recognized to be associated with several disorders, such as obesity, cardiometabolic events, gastrointestinal alterations, and mental diseases, which suggests that intestinal microbes may be a valuable tool as causal or as consequence biomarkers. In this context, the fecal microbiota could also be used as an adequate and informative proxy of the nutritional composition of the food intake and about the adherence to dietary patterns, such as the Mediterranean or Western diets, by displaying specific fecal microbiome signatures. The aim of this review was to discuss the potential use of gut microbial composition as a putative biomarker of food intake and to screen the sensitivity value of fecal microbiota in the evaluation of dietary interventions as a reliable and precise alternative to subjective questionnaires.}, }
@article {pmid36902288, year = {2023}, author = {Pekkala, S}, title = {Fecal Metagenomics and Metabolomics Identifying Microbial Signatures in Non-Alcoholic Fatty Liver Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, doi = {10.3390/ijms24054855}, pmid = {36902288}, issn = {1422-0067}, abstract = {The frequency of non-alcoholic fatty liver disease (NAFLD) has intensified, creating diagnostic challenges and increasing the need for reliable non-invasive diagnostic tools. Due to the importance of the gut-liver axis in the progression of NAFLD, studies attempt to reveal microbial signatures in NAFLD, evaluate them as diagnostic biomarkers, and to predict disease progression. The gut microbiome affects human physiology by processing the ingested food into bioactive metabolites. These molecules can penetrate the portal vein and the liver to promote or prevent hepatic fat accumulation. Here, the findings of human fecal metagenomic and metabolomic studies relating to NAFLD are reviewed. The studies present mostly distinct, and even contradictory, findings regarding microbial metabolites and functional genes in NAFLD. The most abundantly reproducing microbial biomarkers include increased lipopolysaccharides and peptidoglycan biosynthesis, enhanced degradation of lysine, increased levels of branched chain amino acids, as well as altered lipid and carbohydrate metabolism. Among other causes, the discrepancies between the studies may be related to the obesity status of the patients and the severity of NAFLD. In none of the studies, except for one, was diet considered, although it is an important factor driving gut microbiota metabolism. Future studies should consider diet in these analyses.}, }
@article {pmid36901710, year = {2023}, author = {Sobol, MS and Kaster, AK}, title = {Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, doi = {10.3390/ijms24054270}, pmid = {36901710}, issn = {1422-0067}, abstract = {Microbial single-cell genomics (SCG) provides access to the genomes of rare and uncultured microorganisms and is a complementary method to metagenomics. Due to the femtogram-levels of DNA in a single microbial cell, sequencing the genome requires whole genome amplification (WGA) as a preliminary step. However, the most common WGA method, multiple displacement amplification (MDA), is known to be costly and biased against specific genomic regions, preventing high-throughput applications and resulting in uneven genome coverage. Thus, obtaining high-quality genomes from many taxa, especially minority members of microbial communities, becomes difficult. Here, we present a volume reduction approach that significantly reduces costs while improving genome coverage and uniformity of DNA amplification products in standard 384-well plates. Our results demonstrate that further volume reduction in specialized and complex setups (e.g., microfluidic chips) is likely unnecessary to obtain higher-quality microbial genomes. This volume reduction method makes SCG more feasible for future studies, thus helping to broaden our knowledge on the diversity and function of understudied and uncharacterized microorganisms in the environment.}, }
@article {pmid36900663, year = {2023}, author = {de Paz-Silava, SLM and Tabios, IKB and Tantengco, OAG and Climacosa, FMM and Velayo, CL and Lintao, RCV and Cando, LFT and Perias, GAS and Idolor, MIC and Francisco, AG and Catral, CDM and Chiong, CM and Dalmacio, LMM}, title = {Determinants of Acquisition, Persistence, and Clearance of Oncogenic Cervical Human Papillomavirus Infection in the Philippines Using a Multi-Omics Approach: DEFEAT HPV Study Protocol.}, journal = {Healthcare (Basel, Switzerland)}, volume = {11}, number = {5}, pages = {}, doi = {10.3390/healthcare11050658}, pmid = {36900663}, issn = {2227-9032}, abstract = {HPV infection is one of the most studied risk factors in cervical cancer-the second most common cancer site and cause of death due to cancer in the Philippines. However, there is a lack of population-based epidemiological data on cervical HPV infection in the Philippines. Local reports on co-infections with other lower genital tract pathogens, commonly reported globally, are also lacking, which emphasizes the need to increase efforts in targeting HPV prevalence, genotype, and distribution. Hence, we aim to determine the molecular epidemiology and natural history of HPV infection among reproductive-age Filipino women using a community-based prospective cohort design. Women from rural and urban centers will be screened until the target sample size of 110 HPV-positive women (55 from rural sites and 55 from urban sites) is reached. Cervical and vaginal swabs will be collected from all screened participants. For HPV-positive patients, HPV genotypes will be determined. One hundred ten healthy controls will be selected from previously screened volunteers. The cases and controls will comprise the multi-omics subset of participants and will be followed up after 6 and 12 months for repeat HPV screening. Metagenomic and metabolomic analyses of the vaginal swabs will also be performed at baseline, after 6 months, and after 12 months. The results of this study will update the prevalence and genotypic distribution of cervical HPV infection among Filipino women, determine whether the current vaccines used for HPV vaccination programs capture the most prevalent high-risk HPV genotypes in the country, and identify vaginal community state types and bacterial taxa associated with the natural history of cervical HPV infection. The results of this study will be used as the basis for developing a biomarker that can help predict the risk of developing persistent cervical HPV infection in Filipino women.}, }
@article {pmid36900515, year = {2023}, author = {Mancino, W and Carnevali, P and Terzi, V and Pérez, PG and Zhang, L and Giuberti, G and Morelli, L and Patrone, V and Lucini, L}, title = {Hierarchical Effects of Lactic Fermentation and Grain Germination on the Microbial and Metabolomic Profile of Rye Doughs.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/foods12050998}, pmid = {36900515}, issn = {2304-8158}, abstract = {A multi-omics approach was adopted to investigate the impact of lactic acid fermentation and seed germination on the composition and physicochemical properties of rye doughs. Doughs were prepared with either native or germinated rye flour and fermented with Saccharomyces cerevisiae, combined or not with a sourdough starter including Limosilactobacillus fermentum, Weissella confusa and Weissella cibaria. LAB fermentation significantly increased total titrable acidity and dough rise regardless of the flour used. Targeted metagenomics revealed a strong impact of germination on the bacterial community profile of sprouted rye flour. Doughs made with germinated rye displayed higher levels of Latilactobacillus curvatus, while native rye doughs were associated with higher proportions of Lactoplantibacillus plantarum. The oligosaccharide profile of rye doughs indicated a lower carbohydrate content in native doughs as compared to the sprouted counterparts. Mixed fermentation promoted a consistent decrease in both monosaccharides and low-polymerization degree (PD)-oligosaccharides, but not in high-PD carbohydrates. Untargeted metabolomic analysis showed that native and germinated rye doughs differed in the relative abundance of phenolic compounds, terpenoids, and phospholipids. Sourdough fermentation promoted the accumulation of terpenoids, phenolic compounds and proteinogenic and non-proteinogenic amino acids. Present findings offer an integrated perspective on rye dough as a multi-constituent system and on cereal-sourced bioactive compounds potentially affecting the functional properties of derived food products.}, }
@article {pmid36900508, year = {2023}, author = {Coelho, MC and Malcata, FX and Silva, CCG}, title = {Distinct Bacterial Communities in São Jorge Cheese with Protected Designation of Origin (PDO).}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/foods12050990}, pmid = {36900508}, issn = {2304-8158}, abstract = {São Jorge cheese is an iconic product of the Azores, produced from raw cow's milk and natural whey starter (NWS). Although it is produced according to Protected Designation of Origin (PDO) specifications, the granting of the PDO label depends crucially on sensory evaluation by trained tasters. The aim of this work was to characterize the bacterial diversity of this cheese using next-generation sequencing (NGS) and to identify the specific microbiota that contributes most to its uniqueness as a PDO by distinguishing the bacterial communities of PDO and non-PDO cheeses. The NWS and curd microbiota was dominated by Streptococcus and Lactococcus, whereas Lactobacillus and Leuconostoc were also present in the core microbiota of the cheese along with these genera. Significant differences (p < 0.05) in bacterial community composition were found between PDO cheese and non-certified cheese; Leuconostoc was found to play the chief role in this regard. Certified cheeses were richer in Leuconostoc, Lactobacillus and Enterococcus, but had fewer Streptococcus (p < 0.05). A negative correlation was found between contaminating bacteria, e.g., Staphylococcus and Acinetobacter, and the development of PDO-associated bacteria such as Leuconostoc, Lactobacillus and Enterococcus. A reduction in contaminating bacteria was found to be crucial for the development of a bacterial community rich in Leuconostoc and Lactobacillus, thus justifying the PDO seal of quality. This study has helped to clearly distinguish between cheeses with and without PDO based on the composition of the bacterial community. The characterization of the NWS and the cheese microbiota can contribute to a better understanding of the microbial dynamics of this traditional PDO cheese and can help producers interested in maintaining the identity and quality of São Jorge PDO cheese.}, }
@article {pmid36898564, year = {2023}, author = {Xu, Y and Meng, X and Song, Y and Lv, X and Sun, Y}, title = {Effects of different concentrations of butyrate on microbial community construction and metabolic pathways in anaerobic digestion.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {128845}, doi = {10.1016/j.biortech.2023.128845}, pmid = {36898564}, issn = {1873-2976}, abstract = {Investigating the effect of butyric acid concentration on anaerobic digestion systems in complex systems is important for the efficient degradation of butyric acid and improving the efficiency of anaerobic digestion. In this study, different loadings of butyric acid with 2.8, 3.2, and 3.6 g/(L·d) were added to the anaerobic reactor. At a high organic loading rate of 3.6 g/(L·d), methane was efficiently produced with VBP (Volumetric Biogas Production) of 1.50 L/(L·d) and biogas content between 65% to 75%. VFAs concentration remained below 2000 mg/L. Metagenome sequencing revealed changes in the functional flora within different stages. Methanosarcina, Syntrophomonas, and Lentimicrobium were the main and functional microorganisms. That the relative abundance of methanogens exceeded 35% and methanogenic metabolic pathways were increased indicated the methanogenic capacity of the system significantly improved. The presence of a large number of hydrolytic acid-producing bacteria also indicated the importance of the hydrolytic acid-producing stage in the system.}, }
@article {pmid36898310, year = {2023}, author = {Hu, X and Gu, H and Sun, X and Wang, Y and Liu, J and Yu, Z and Li, Y and Jin, J and Wang, G}, title = {Distinct influence of conventional and biodegradable microplastics on microbe-driving nitrogen cycling processes in soils and plastispheres as evaluated by metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131097}, doi = {10.1016/j.jhazmat.2023.131097}, pmid = {36898310}, issn = {1873-3336}, abstract = {Plastic mulching is one of the large contributors to microplastic (MP) accumulation in agricultural landscapes. However, the effects of conventional (PE-MPs) and biodegradable MPs (BMPs) on microbial functional and genomic information encoding nitrogen (N) cycling have yet to be addressed. Here, a soil microcosmic experiment was conducted by adding PE-MPs and BMPs to a Mollisol at dosage of 5% (w/w) followed by incubation for 90 days. The soils and MPs were examined by metagenomics and genome binning methods. The results revealed that BMPs harbored rougher surfaces and induced stronger alterations in microbial functional and taxonomic profiles in the soil and plastisphere than PE-MPs. In comparison to their respective soils, the plastispheres of PE-MPs and BMPs stimulated the processes of N fixation, N degradation and assimilatory nitrate reduction (ANRA) and reduced the gene abundances encoding nitrification and denitrification, in which BMPs induced stronger influences than PE-MPs. Ramlibacter mainly drove the differences in N cycling processes between the soils containing two types of MPs and was further enriched in the BMP plastisphere. Three high-quality genomes were identified as Ramlibacter stains with higher abundances in the plastisphere of BMP than that of PE-MP. These Ramlibacter strains had the metabolic capacities of N fixation, N degradation, ANRA and ammonium transport, which were potentially attributed to their biosynthesis and the accumulation of soil NH4[+]-N. Taken together, our results highlight the genetic mechanisms of soil N bioavailability in the presence of biodegradable MPs, which have important implications for maintaining sustainable agriculture and controlling microplastic risk.}, }
@article {pmid36897935, year = {2023}, author = {Carr, VR and Pissis, SP and Mullany, P and Shoaie, S and Gomez-Cabrero, D and Moyes, DL}, title = {Palidis: fast discovery of novel insertion sequences.}, journal = {Microbial genomics}, volume = {9}, number = {3}, pages = {}, doi = {10.1099/mgen.0.000917}, pmid = {36897935}, issn = {2057-5858}, abstract = {The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinformatics pipeline called Palidis that recognizes insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterized. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences.}, }
@article {pmid36896778, year = {2023}, author = {Obregon Alvarez, D and Fonseca de Souza, L and Mendes, LW and de Moraes, MT and Tosi, M and Venturini, AM and Meyer, KM and Barbosa de Camargo, P and Bohannan, BJM and Rodrigues, JLM and Dunfield, KE and Tsai, SM}, title = {Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16912}, pmid = {36896778}, issn = {1365-294X}, abstract = {Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with in situ CH4 fluxes and soil edaphic factors measurements and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harboring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity, and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.}, }
@article {pmid36894986, year = {2023}, author = {de Nies, L and Galata, V and Martin-Gallausiaux, C and Despotovic, M and Busi, SB and Snoeck, CJ and Delacour, L and Budagavi, DP and Laczny, CC and Habier, J and Lupu, PC and Halder, R and Fritz, JV and Marques, T and Sandt, E and O'Sullivan, MP and Ghosh, S and Satagopam, V and ,  and Krüger, R and Fagherazzi, G and Ollert, M and Hefeng, FQ and May, P and Wilmes, P}, title = {Altered infective competence of the human gut microbiome in COVID-19.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {46}, pmid = {36894986}, issn = {2049-2618}, abstract = {BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.<br><br>RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls.<br><br>CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.}, }
@article {pmid36894760, year = {2023}, author = {Sajid, M and Srivastava, S and Yadav, RK and Joshi, L and Bharadwaj, M}, title = {Fungal Community Composition and Function Associated with Loose Smokeless Tobacco Products.}, journal = {Current microbiology}, volume = {80}, number = {4}, pages = {131}, pmid = {36894760}, issn = {1432-0991}, abstract = {Smokeless tobacco products (STPs) contain several microbial communities which are responsible for the formation of carcinogens, like tobacco-specific nitrosamine (TSNAs). A majority of STPs are sold in loose/unpackaged form which can be loaded with a diverse microbial population. Here, the fungal population and mycotoxins level of three popular Indian loose STPs, Dohra, Mainpuri Kapoori (MK), and loose leaf-chewing tobacco (LCT) was examined using metagenomic sequencing of ITS1 DNA segment of the fungal genome and LC-MS/MS, respectively. We observed that Ascomycota was the most abundant phylum and Sterigmatomyces and Pichia were the predominant fungal genera in loose STPs. MK displayed the highest α-diversity being enriched with pathogenic fungi Apiotrichum, Aspergillus, Candida, Fusarium, Trichosporon, and Wallemia. Further, FUNGuild analysis revealed an abundance of saprotrophs in MK, while pathogen-saprotroph-symbiotroph were abundant in Dohra and LCT. The level of a fungal toxin (ochratoxins A) was high in the MK product. This study caution that loose STPs harbor various harmful fungi that can infect their users and deliver fungal toxins or disrupt the oral microbiome of SLT users which can contribute to several oral pathologies.}, }
@article {pmid36894632, year = {2023}, author = {Molari, M and Hassenrueck, C and Laso-Pérez, R and Wegener, G and Offre, P and Scilipoti, S and Boetius, A}, title = {A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {36894632}, issn = {2058-5276}, abstract = {Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonas from the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, [U]Sulfurimonas pluma, was found to be globally abundant and active in cold (<0-4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes. Compared with other Sulfurimonas species, [U]S. pluma has a reduced genome (>17%) and genomic signatures of an aerobic chemolithotrophic metabolism using hydrogen as an energy source, including acquisition of A2-type oxidase and loss of nitrate and nitrite reductases. The dominance and unique niche of [U]S. pluma in hydrothermal plumes suggest an unappreciated biogeochemical role for Sulfurimonas in the deep ocean.}, }
@article {pmid36894532, year = {2023}, author = {Sukumar, S and Wang, F and Simpson, CA and Willet, CE and Chew, T and Hughes, TE and Bockmann, MR and Sadsad, R and Martin, FE and Lydecker, HW and Browne, GV and Davis, KM and Bui, M and Martinez, E and Adler, CJ}, title = {Development of the oral resistome during the first decade of life.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1291}, pmid = {36894532}, issn = {2041-1723}, abstract = {Antibiotic overuse has promoted the spread of antimicrobial resistance (AMR) with significant health and economic consequences. Genome sequencing reveals the widespread presence of antimicrobial resistance genes (ARGs) in diverse microbial environments. Hence, surveillance of resistance reservoirs, like the rarely explored oral microbiome, is necessary to combat AMR. Here, we characterise the development of the paediatric oral resistome and investigate its role in dental caries in 221 twin children (124 females and 97 males) sampled at three time points over the first decade of life. From 530 oral metagenomes, we identify 309 ARGs, which significantly cluster by age, with host genetic effects detected from infancy onwards. Our results suggest potential mobilisation of ARGs increases with age as the AMR associated mobile genetic element, Tn916 transposase was co-located with more species and ARGs in older children. We find a depletion of ARGs and species in dental caries compared to health. This trend reverses in restored teeth. Here we show the paediatric oral resistome is an inherent and dynamic component of the oral microbiome, with a potential role in transmission of AMR and dysbiosis.}, }
@article {pmid36893594, year = {2023}, author = {Saibu, S and Adebusoye, SA and Oyetibo, GO}, title = {Soil microbiome response to 2-chlorodibenzo-p-dioxin during bioremediation of contaminated tropical soil in a microcosm-based study.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131105}, doi = {10.1016/j.jhazmat.2023.131105}, pmid = {36893594}, issn = {1873-3336}, abstract = {A pristine soil was artificially contaminated with 2-chlorodibenzo-p-dioxin (2-CDD) and separated into three portions. Microcosms SSOC and SSCC were seeded with Bacillus sp. SS2 and a three-member bacterial consortium respectively; SSC was untreated, while heat-sterilized contaminated soil served as overall control. Significant degradation of 2-CDD occurred in all microcosms except for the control where the concentration remained unchanged. Degradation of 2-CDD was highest in SSCC (94.9%) compared to SSOC (91.66%) and SCC (85.9%). There was also a notable reduction in the microbial composition complexity both in species richness and evenness following dioxin contamination, a trend that nearly lasted the study period; particularly in setups SSC and SSOC. Irrespective of the bioremediation strategies, the soil microflora was practically dominated by the Firmicutes and at the genus level, the phylotype Bacillus was the most dominant. Other dominant taxa though negatively impacted were Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria. Overall, this study demonstrated the feasibility of microbial seeding as an effective strategy to cleanup tropical soil contaminated with dioxins and the importance of metagenomics in elucidating the microbial diversities of contaminated soils. Meanwhile, the seeded organisms, owed their success not only to metabolic competence, but survivability, adaptability and ability to compete favourably with autochthonous microflora.}, }
@article {pmid36892439, year = {2023}, author = {Jain, C}, title = {Coverage-preserving sparsification of overlap graphs for long-read assembly.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad124}, pmid = {36892439}, issn = {1367-4811}, abstract = {UNLABELLED: Read-overlap-based graph data structures play a central role in computing de novo genome assembly. Most long-read assemblers use Myers's string graph model to sparsify overlap graphs. Graph sparsification improves assembly contiguity by removing spurious and redundant connections. However, a graph model must be coverage-preserving, i.e., it must ensure that there exist walks in the graph that spell all chromosomes, given sufficient sequencing coverage. This property becomes even more important for diploid genomes, polyploid genomes and metagenomes where there is a risk of losing haplotype-specific information.We develop a novel theoretical framework under which the coverage-preserving properties of a graph model can be analysed. We first prove that de Bruijn graph and overlap graph models are guaranteed to be coverage-preserving. We next show that the standard string graph model lacks this guarantee. The latter result is consistent with the observation made in (Hui et al., 2016) that removal of contained reads, i.e., the reads that are substrings of other reads, can lead to coverage gaps during string graph construction. Our experiments done using simulated long reads from HG002 human diploid genome show that 50 coverage gaps are introduced on average by ignoring contained reads from nanopore datasets. To remedy this, we propose practical heuristics that are well-supported by our theoretical results, and are useful to decide which contained reads should be retained to avoid coverage gaps. Our method retains a small fraction of contained reads (1 - 2%) and closes majority of the coverage gaps.<br><br>IMPLEMENTATION: Source code is available through GitHub (https://github.com/at-cg/ContainX) and Zenodo with doi: 10.5281/zenodo.7687543.}, }
@article {pmid36892308, year = {2023}, author = {Pienkowska, K and Pust, MM and Gessner, M and Gaedcke, S and Thavarasa, A and Rosenboom, I and Morán Losada, P and Minso, R and Arnold, C and Hedtfeld, S and Dorda, M and Wiehlmann, L and Mainz, JG and Klockgether, J and Tümmler, B}, title = {The Cystic Fibrosis Upper and Lower Airway Metagenome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0363322}, doi = {10.1128/spectrum.03633-22}, pmid = {36892308}, issn = {2165-0497}, abstract = {The microbial metagenome in cystic fibrosis (CF) airways was investigated by whole-genome shotgun sequencing of total DNA isolated from nasal lavage samples, oropharyngeal swabs, and induced sputum samples collected from 65 individuals with CF aged 7 to 50 years. Each patient harbored a personalized microbial metagenome unique in microbial load and composition, the exception being monocultures of the most common CF pathogens Staphylococcus aureus and Pseudomonas aeruginosa from patients with advanced lung disease. The sampling of the upper airways by nasal lavage uncovered the fungus Malassezia restricta and the bacterium Staphylococcus epidermidis as prominent species. Healthy and CF donors harbored qualitatively and quantitatively different spectra of commensal bacteria in their sputa, even in the absence of any typical CF pathogen. If P. aeruginosa, S. aureus, or Stenotrophomonas maltophilia belonged to the trio of the most abundant species in the CF sputum metagenome, common inhabitants of the respiratory tract of healthy subjects, i.e., Eubacterium sulci, Fusobacterium periodonticum, and Neisseria subflava, were present only in low numbers or not detectable. Random forest analysis identified the numerical ecological parameters of the bacterial community, such as Shannon and Simpson diversity, as the key parameters that globally distinguish sputum samples from CF and healthy donors. IMPORTANCE Cystic fibrosis (CF) is the most common life-limiting monogenetic disease in European populations and is caused by mutations in the CFTR gene. Chronic airway infections with opportunistic pathogens are the major morbidity that determines prognosis and quality of life in most people with CF. We examined the composition of the microbial communities of the oral cavity and upper and lower airways in CF patients across all age groups. From early on, the spectrum of commensals is different in health and CF. Later on, when the common CF pathogens take up residence in the lungs, we observed differential modes of depletion of the commensal microbiota in the presence of S. aureus, P. aeruginosa, S. maltophilia, or combinations thereof. It remains to be seen whether the implementation of lifelong CFTR (cystic fibrosis transmembrane conductance regulator) modulation will change the temporal evolution of the CF airway metagenome.}, }
@article {pmid36892203, year = {2023}, author = {Taoka, A and Eguchi, Y and Shimoshige, R and Fukumori, Y}, title = {Recent advances in studies on magnetosome-associated proteins composing the bacterial geomagnetic sensor organelle.}, journal = {Microbiology and immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1348-0421.13062}, pmid = {36892203}, issn = {1348-0421}, abstract = {Magnetotactic bacteria (MTB) generate a membrane-enclosed subcellular compartment called magnetosome, which contains a biomineralized magnetite or greigite crystal, an inner membrane-derived lipid bilayer membrane, and a set of specifically targeted associated proteins. Magnetosomes are formed by a group of magnetosome-associated proteins encoded in a genomic region called magnetosome island. Magnetosomes are then arranged in a linear chain-like positioning, and the resulting magnetic dipole of the chain functions as a geomagnetic sensor for magneto-aerotaxis motility. Recent metagenomic analyses of environmental specimens shed light on the sizable phylogenetical diversity of uncultured MTB at the phylum level. These findings have led to a better understanding of the diversity and conservation of magnetosome-associated proteins. This review provided an overview of magnetosomes and magnetosome-associated proteins and introduced recent topics about this fascinating magnetic bacterial organelle. This article is protected by copyright. All rights reserved.}, }
@article {pmid36891384, year = {2023}, author = {Wang, B and Wang, X and Wang, Z and Zhu, K and Wu, W}, title = {Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1102547}, pmid = {36891384}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil salinization is a serious abiotic stress for grapevines. The rhizosphere microbiota of plants can help counter the negative effects caused by salt stress, but the distinction between rhizosphere microbes of salt-tolerant and salt-sensitive varieties remains unclear.<br><br>METHODS: This study employed metagenomic sequencing to explore the rhizosphere microbial community of grapevine rootstocks 101-14 (salt tolerant) and 5BB (salt sensitive) with or without salt stress.<br><br>RESULTS AND DISCUSSION: Compared to the control (treated with ddH2O), salt stress induced greater changes in the rhizosphere microbiota of 101-14 than in that of 5BB. The relative abundances of more plant growth-promoting bacteria, including Planctomycetes, Bacteroidetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Chloroflexi, and Firmicutes, were increased in 101-14 under salt stress, whereas only the relative abundances of four phyla (Actinobacteria, Gemmatimonadetes, Chloroflexi, and Cyanobacteria) were increased in 5BB under salt stress while those of three phyla (Acidobacteria, Verrucomicrobia, and Firmicutes) were depleted. The differentially enriched functions (KEGG level 2) in 101-14 were mainly associated with pathways related to cell motility; folding, sorting, and degradation functions; glycan biosynthesis and metabolism; xenobiotics biodegradation and metabolism; and metabolism of cofactors and vitamins, whereas only the translation function was differentially enriched in 5BB. Under salt stress, the rhizosphere microbiota functions of 101-14 and 5BB differed greatly, especially pathways related to metabolism. Further analysis revealed that pathways associated with sulfur and glutathione metabolism as well as bacterial chemotaxis were uniquely enriched in 101-14 under salt stress and therefore might play vital roles in the mitigation of salt stress on grapevines. In addition, the abundance of various sulfur cycle-related genes, including genes involved in assimilatory sulfate reduction (cysNC, cysQ, sat, and sir), sulfur reduction (fsr), SOX systems (soxB), sulfur oxidation (sqr), organic sulfur transformation (tpa, mdh, gdh, and betC), increased significantly in 101-14 after treatment with NaCl; these genes might mitigate the harmful effects of salt on grapevine. In short, the study findings indicate that both the composition and functions of the rhizosphere microbial community contribute to the enhanced tolerance of some grapevines to salt stress.}, }
@article {pmid36891307, year = {2023}, author = {Yang, Q and Yu, C and Wu, Y and Cao, K and Li, X and Cao, W and Cao, L and Zhang, S and Ba, Y and Zheng, Y and Zhang, H and Wang, W}, title = {Unusual Talaromyces marneffei and Pneumocystis jirovecii coinfection in a child with a STAT1 mutation: A case report and literature review.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1103184}, pmid = {36891307}, issn = {1664-3224}, abstract = {Talaromyces marneffei and Pneumocystis jirovecii are the common opportunistic pathogens in immunodeficient patients. There have been no reports of T. marneffei and P. jirovecii coinfection in immunodeficient children. Signal transducer and activator of transcription 1 (STAT1) is a key transcription factor in immune responses. STAT1 mutations are predominately associated with chronic mucocutaneous candidiasis and invasive mycosis. We report a 1-year-2-month-old boy diagnosed with severe laryngitis and pneumonia caused by T. marneffei and P. jirovecii coinfection, which was confirmed by smear, culture, polymerase chain reaction and metagenome next-generation sequencing of bronchoalveolar lavage fluid. He has a known STAT1 mutation at amino acid 274 in the coiled-coil domain of STAT1 according to whole exome sequencing. Based on the pathogen results, itraconazole and trimethoprim-sulfamethoxazole were administered. This patient's condition improved, and he was discharged after two weeks of targeted therapy. In the one-year follow-up, the boy remained symptom-free without recurrence.}, }
@article {pmid36891192, year = {2023}, author = {Jeong, J and Ahn, K and Mun, S and Yun, K and Kim, YT and Jung, W and Lee, KE and Kim, MY and Ahn, Y and Han, K}, title = {Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans.}, journal = {Journal of oral microbiology}, volume = {15}, number = {1}, pages = {2186591}, pmid = {36891192}, issn = {2000-2297}, abstract = {Oral microbial ecosystem could influence intestinal diseases, but there have been insufficient studies demonstrating the association of microbial composition between the oral cavity and the intestinal system. Thus, we aimed to investigate the compositional network within the oral microbiome related to gut enterotype from saliva and stool samples collected from 112 healthy Korean subjects. Here, we performed bacterial 16S amplicon sequencing from clinical samples. Then, we determined oral microbiome type related to individual's gut enterotype for healthy Korean. The co-occurrence analysis was performed to interactivity prediction of microbiome within saliva samples. As a result, it could be classified into two Korean oral microbiome types (KO) and four oral-gut-associated microbiome types (KOGA) according to distribution and significant differences of oral microflora. The co-occurrence analysis showed various bacterial compositional networks linked around Streptococcus and Haemophilus within healthy subjects. The present study was first approach in healthy Koreans to identify the oral microbiome types related to the gut microbiome and investigate their characteristics. Hence, we suggest that our results could be potential healthy control data for identifying differences in microbial composition between healthy people and oral disease patients and studying microbial association with the gut microbial environment (oral-gut microbiome axis).}, }
@article {pmid36891155, year = {2023}, author = {Liu, G and Wang, L and Li, X and Zhang, Y and Long, H and Wang, Y and Gao, H and Xia, H and Qian, S}, title = {The value of next-generation metagenomic sequencing in pathogen detection of pleural effusions and ascites from children with sepsis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1130483}, pmid = {36891155}, issn = {2235-2988}, abstract = {OBJECTIVE: To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) using pleural effusion and ascites from children with sepsis.<br><br>METHODS: In this study, children with sepsis or severe sepsis and appeared pleural or peritoneal effusions were enrolled, of whom the pleural effusions or ascites and blood samples were conducted pathogen detection using both conventional and mNGS methods. The samples were divided into pathogen-consistent and pathogen-inconsistent groups based on the consistency of mNGS results from different sample types, and into exudate and transudate groups based on their pleural effusion and ascites properties. The pathogen positive rates, pathogen spectrum, consistency between different sample types, and clinical diagnosis consistency were compared between mNGS and conventional pathogen tests.<br><br>RESULTS: A total of 42 pleural effusions or ascites and 50 other type samples were collected from 32 children. The pathogen positive rate of the mNGS test was significantly higher than that of traditional methods (78.57% vs. 14.29%, P < 0.001) in pleural effusion and ascites samples, with a consistent rate of 66.67% between the two methods. Nearly 78.79% (26/33) of mNGS positive results of the pleural effusions and ascites samples were consistent with clinical evaluation, and 81.82% (27/33) of these positive samples reported 1-3 pathogens. The pathogen-consistent group outperformed the pathogen-inconsistent group in terms of consistency with respect to clinical evaluation (88.46% vs. 57.14%, P = 0.093), while there was no significant difference between the exudate and transudate groups (66.67% vs. 50.00%, P = 0.483).<br><br>CONCLUSION: Compared to conventional methods, mNGS has great advantages in pathogen detection of pleural effusion and ascites samples. Moreover, consistent results of mNGS tests with different sample types provide more reference values in clinical diagnosis.}, }
@article {pmid36890606, year = {2023}, author = {Li, X and Zhao, R and Li, D and Wang, G and Bei, S and Ju, X and An, R and Li, L and Kuyper, TW and Christie, P and Bender, FS and Veen, C and van der Heijden, MGA and van der Putten, WH and Zhang, F and Butterbach-Bahl, K and Zhang, J}, title = {Mycorrhiza-mediated recruitment of complete denitrifying Pseudomonas reduces N2O emissions from soil.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {45}, pmid = {36890606}, issn = {2049-2618}, abstract = {BACKGROUND: Arbuscular mycorrhizal fungi (AMF) are key soil organisms and their extensive hyphae create a unique hyphosphere associated with microbes actively involved in N cycling. However, the underlying mechanisms how AMF and hyphae-associated microbes may cooperate to influence N2O emissions from "hot spot" residue patches remain unclear. Here we explored the key microbes in the hyphosphere involved in N2O production and consumption using amplicon and shotgun metagenomic sequencing. Chemotaxis, growth and N2O emissions of isolated N2O-reducing bacteria in response to hyphal exudates were tested using in vitro cultures and inoculation experiments.<br><br>RESULTS: AMF hyphae reduced denitrification-derived N2O emission (max. 63%) in C- and N-rich residue patches. AMF consistently enhanced the abundance and expression of clade I nosZ gene, and inconsistently increased that of nirS and nirK genes. The reduction of N2O emissions in the hyphosphere was linked to N2O-reducing Pseudomonas specifically enriched by AMF, concurring with the increase in the relative abundance of the key genes involved in bacterial citrate cycle. Phenotypic characterization of the isolated complete denitrifying P. fluorescens strain JL1 (possessing&#xa0;clade I nosZ) indicated that the decline of net N2O emission was a result of upregulated nosZ expression in P. fluorescens following hyphal exudation (e.g. carboxylates). These findings were further validated by re-inoculating sterilized residue patches with P. fluorescens and by an 11-year-long field experiment showing significant positive correlation between hyphal length density with the abundance of clade I nosZ gene.<br><br>CONCLUSIONS: The cooperation between AMF and the N2O-reducing Pseudomonas residing on hyphae significantly reduce N2O emissions in the microsites. Carboxylates exuded by hyphae act as attractants in recruiting P. fluorescens and also as stimulants triggering nosZ gene expression. Our discovery indicates that reinforcing synergies between AMF and hyphosphere microbiome may provide unexplored opportunities to stimulate N2O consumption in nutrient-enriched microsites, and consequently reduce N2O emissions from soils. This knowledge opens novel avenues to exploit cross-kingdom microbial interactions for sustainable agriculture and for climate change mitigation. Video Abstract.}, }
@article {pmid36890583, year = {2023}, author = {Burks, DJ and Pusadkar, V and Azad, RK}, title = {POSMM: an efficient alignment-free metagenomic profiler that complements alignment-based profiling.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {16}, pmid = {36890583}, issn = {2524-6372}, abstract = {We present here POSMM (pronounced 'Possum'), Python-Optimized Standard Markov Model classifier, which is a new incarnation of the Markov model approach to metagenomic sequence analysis. Built on the top of a rapid Markov model based classification algorithm SMM, POSMM reintroduces high sensitivity associated with alignment-free taxonomic classifiers to probe whole genome or metagenome datasets of increasingly prohibitive sizes. Logistic regression models generated and optimized using the Python sklearn library, transform Markov model probabilities to scores suitable for thresholding. Featuring a dynamic database-free approach, models are generated directly from genome fasta files per run, making POSMM a valuable accompaniment to many other programs. By combining POSMM with ultrafast classifiers such as Kraken2, their complementary strengths can be leveraged to produce higher overall accuracy in metagenomic sequence classification than by either as a standalone classifier. POSMM is a user-friendly and highly adaptable tool designed for broad use by the metagenome scientific community.}, }
@article {pmid36890581, year = {2023}, author = {Shi, J and Lei, Y and Wu, J and Li, Z and Zhang, X and Jia, L and Wang, Y and Ma, Y and Zhang, K and Cheng, Q and Zhang, Z and Ma, Y and Lei, Z}, title = {Antimicrobial peptides act on the rumen microbiome and metabolome affecting the performance of castrated bulls.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {31}, pmid = {36890581}, issn = {1674-9782}, abstract = {BACKGROUND: Many countries have already banned the use of antibiotics in animal husbandry, making it extremely difficult to maintain animal health in livestock breeding. In the livestock industry, there is an urgent need to develop alternatives to antibiotics which will not lead to drug resistance on prolonged use. In this study, eighteen castrated bulls were randomly divided into two groups. The control group (CK) was fed the basal diet, while the antimicrobial peptide group (AP) was fed the basal diet supplemented with 8 g of antimicrobial peptides in the basal diet for the experimental period of 270 d. They were then slaughtered to measure production performance, and the ruminal contents were isolated for metagenomic and metabolome sequencing analysis.<br><br>RESULT: The results showed that antimicrobial peptides could improve the daily weight, carcass weight, and net meat weight of the experimental animals. Additionally, the rumen papillae diameter and the micropapillary density in the AP were significantly greater than those&#xa0;in the CK. Furthermore, the determination of digestive enzymes and fermentation parameters showed that the contents of protease, xylanase, and &#x3b2;-glucoside in the AP were greater than those in the CK. However, lipase content in the CK was greater than that in the AP. Moreover, the content of acetate, propionate, butyrate, and valerate was found to be greater in AP than those&#xa0;in CK. The metagenomic analysis annotated 1993 differential microorganisms at the species level. The KEGG enrichment of these microorganisms revealed that the enrichment of drug resistance-related pathways was dramatically decreased in the AP, whereas the enrichment of immune-related pathways was significantly increased. There was also a significant reduction in the types of viruses in the AP. 187 probiotics with significant differences were found, 135 of which were higher in AP than in CK. It was also found that the antimicrobial mechanism of the antimicrobial peptides was quite specific. Seven low-abundance microorganisms (Acinetobacter_sp._Ac_1271, Aequorivita soesokkakensis, Bacillus lacisalsi, Haloferax larsenii, Lysinibacillus_sp._3DF0063, Parabacteroides_sp._2_1_7, Streptomyces_sp._So13.3) were found to regulate growth performance of the bull negatively. Metabolome analysis identified 45 differentially differential metabolites that significantly different between the CK and the AP groups. Seven upregulated metabolites (4-pyridoxic acid, Ala-Phe, 3-ureidopropionate, hippuric acid, terephthalic acid, L-alanine, uridine 5-monophosphate) improve the growth performance of the experimental animals. To detect the interactions between the rumen microbiome and metabolism, we associated the rumen microbiome with the metabolome and found that negative regulation between the above 7 microorganisms and 7 metabolites.<br><br>CONCLUSIONS: This study shows that antimicrobial peptides can improve the growth performance of animals while resisting viruses and harmful bacteria and are expected to become healthy alternatives to antibiotics. We demonstrated a new antimicrobial peptides pharmacological model. We demonstrated low-abundance microorganisms may play a role by regulating the content of metabolites.}, }
@article {pmid36890518, year = {2023}, author = {McDew-White, M and Lee, E and Premadasa, LS and Alvarez, X and Okeoma, CM and Mohan, M}, title = {Cannabinoids modulate the microbiota-gut-brain axis in HIV/SIV infection by reducing neuroinflammation and dysbiosis while concurrently elevating endocannabinoid and indole-3-propionate levels.}, journal = {Journal of neuroinflammation}, volume = {20}, number = {1}, pages = {62}, pmid = {36890518}, issn = {1742-2094}, abstract = {BACKGROUND: Although the advent of combination anti-retroviral therapy (cART) has transformed HIV into a manageable chronic disease, an estimated 30-50% of people living with HIV (PLWH) exhibit cognitive and motor deficits collectively known as HIV-associated neurocognitive disorders (HAND). A key driver of HAND neuropathology is chronic neuroinflammation, where proinflammatory mediators produced by activated microglia and macrophages are thought to inflict neuronal injury and loss. Moreover, the dysregulation of the microbiota-gut-brain axis (MGBA) in PLWH, consequent to gastrointestinal dysfunction and dysbiosis, can lead to neuroinflammation and persistent cognitive impairment, which underscores the need for new interventions.<br><br>METHODS: We performed RNA-seq and microRNA profiling in basal ganglia (BG), metabolomics (plasma) and shotgun&#xa0;metagenomic&#xa0;sequencing&#xa0;(colon contents) in uninfected and SIV-infected rhesus macaques (RMs) administered vehicle (VEH/SIV) or delta-9-tetrahydrocannabinol (THC) (THC/SIV).<br><br>RESULTS: Long-term, low-dose THC reduced neuroinflammation and dysbiosis and significantly increased plasma endocannabinoid, endocannabinoid-like, glycerophospholipid and indole-3-propionate levels in chronically SIV-infected RMs. Chronic THC potently blocked the upregulation of genes associated with type-I interferon responses (NLRC5, CCL2, CXCL10, IRF1, IRF7, STAT2, BST2), excitotoxicity (SLC7A11), and enhanced protein expression of WFS1 (endoplasmic reticulum stress) and CRYM (oxidative stress) in BG. Additionally, THC successfully countered miR-142-3p-mediated suppression of WFS1 protein expression via a cannabinoid receptor-1-mediated mechanism in HCN2 neuronal cells. Most importantly, THC significantly increased the relative abundance of Firmicutes and Clostridia including indole-3-propionate (C. botulinum, C. paraputrificum, and C. cadaveris) and butyrate (C. butyricum, Faecalibacterium prausnitzii and Butyricicoccus pullicaecorum) producers in colonic contents.<br><br>CONCLUSION: This study demonstrates the potential of long-term, low-dose THC to positively modulate the MGBA by reducing neuroinflammation, enhancing endocannabinoid levels and promoting the growth of gut bacterial species that produce neuroprotective metabolites, like indole-3-propionate. The findings from this study may benefit not only PLWH on cART, but also those with no access to cART and more importantly, those who fail to suppress the virus under cART.}, }
@article {pmid36799935, year = {2023}, author = {Cao, L and Dai, Z and Tan, H and Zheng, H and Wang, Y and Chen, J and Kuang, H and Chong, RA and Han, M and Hu, F and Sun, W and Sun, C and Zhang, Z}, title = {Population Structure, Demographic History, and Adaptation of Giant Honeybees in China Revealed by Population Genomic Data.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36799935}, issn = {1759-6653}, mesh = {Bees/genetics ; Animals ; Humans ; Phylogeny ; *Metagenomics ; *Adaptation, Physiological/genetics ; China ; Demography ; }, abstract = {There have been many population-based genomic studies on human-managed honeybees (Apis mellifera and Apis cerana), but there has been a notable lack of analysis with regard to wild honeybees, particularly in relation to their evolutionary history. Nevertheless, giant honeybees have been found to occupy distinct habitats and display remarkable characteristics, which are attracting an increased amount of attention. In this study, we de novo sequenced and then assembled the draft genome sequence of the Himalayan giant honeybee, Apis laboriosa. Phylogenetic analysis based on genomic information indicated that A. laboriosa and its tropical sister species Apis dorsata diverged ∼2.61 Ma, which supports the speciation hypothesis that links A. laboriosa to geological changes throughout history. Furthermore, we re-sequenced A. laboriosa and A. dorsata samples from five and six regions, respectively, across their population ranges in China. These analyses highlighted major genetic differences for Tibetan A. laboriosa as well as the Hainan Island A. dorsata. The demographic history of most giant honeybee populations has mirrored glacial cycles. More importantly, contrary to what has occurred among human-managed honeybees, the demographic history of these two wild honeybee species indicates a rapid decline in effective population size in the recent past, reflecting their differences in evolutionary histories. Several genes were found to be subject to selection, which may help giant honeybees to adapt to specific local conditions. In summary, our study sheds light on the evolutionary and adaptational characteristics of two wild giant honeybee species, which was useful for giant honeybee conservation.}, }
@article {pmid35398939, year = {2023}, author = {Zhang, L and Chaturvedi, S and Nice, CC and Lucas, LK and Gompert, Z}, title = {Population genomic evidence of selection on structural variants in a natural hybrid zone.}, journal = {Molecular ecology}, volume = {32}, number = {6}, pages = {1497-1514}, doi = {10.1111/mec.16469}, pmid = {35398939}, issn = {1365-294X}, mesh = {*Metagenomics ; *Genomics ; Genetic Drift ; Polymorphism, Single Nucleotide/genetics ; Reproductive Isolation ; }, abstract = {Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson Hole Lycaeides) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviated from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole Lycaeides ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average than SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess ancestry from Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might disproportionately affect hybrid fitness and thus contribute to reproductive isolation.}, }
@article {pmid36891249, year = {2022}, author = {Bawaneh, A and Shively, CA and Tooze, JA and Cook, KL}, title = {Impact of gut permeability on the breast microbiome using a non-human primate model.}, journal = {Gut microbiome (Cambridge, England)}, volume = {3}, number = {}, pages = {}, pmid = {36891249}, issn = {2632-2897}, abstract = {We previously demonstrated in non-human primates (NHP) that Mediterranean diet consumption shifted the proportional abundance of Lactobacillus in the breast and gut. This data highlights a potential link about gut-breast microbiome interconnectivity. To address this question, we compared bacterial populations identified in matched breast and faecal samples from our NHP study. Dietary pattern concurrently shifted two species in both regions; Streptococcus lutetiensis and Ruminococcus torques. While we observe similar trends in Lactobacillus abundances in the breast and gut, the species identified in each region vary; Mediterranean diet increased Lactobacillus_unspecified species in breast but regulated L. animalis and L. reuteri in the gut.We also investigated the impact of gut permeability on the breast microbiome. Regardless of dietary pattern, subjects that displayed increased physiological measures of gut permeability (elevated plasma lipopolysaccharide, decreased villi length, and decreased goblet cells) displayed a significantly different breast microbiome. Gut barrier dysfunction was associated with increased α-diversity and significant different β-diversity in the breast tissue. Taken together our data supports the presence of a breast microbiome influenced by diet that largely varies from the gut microbiome population but is, however, sensitive to gut permeability.}, }
@article {pmid36890285, year = {2023}, author = {de Sousa, LP and Filho, OG and Mondego, JMC}, title = {Age-Related Rhizosphere Analysis of Coffea arabica Plants.}, journal = {Current microbiology}, volume = {80}, number = {4}, pages = {130}, pmid = {36890285}, issn = {1432-0991}, abstract = {The analysis of large-scale sequence data has revealed that plants over time recruit certain microbes that are efficient colonizers of the rhizosphere. This enrichment phenomenon is especially seen in annual crops, but we suggest that there could have been some type of enrichment in perennial crops such as coffee plants. To verify this hypothesis, we performed a metagenomic and chemical analysis in rhizosphere with three different plant ages (young, mature, and old) and cultivated on the same farm. We verified that from mature to old plants, there was a decrease in diversity, particularly Fusarium and Plenodomus, while there was an increase in Aspergillus, Cladosporium, Metarhizium, and Pseudomonas. We also detected that the abundance of anti-microbials and ACC-deaminase grows as plants age, although denitrification and carbon fixation had reduced abundances. In summary, we detected an enrichment in the microbial community, especially in the great increase in the participation of Pseudomonas, passing from 50% of the relative abundance as the plants get older. Such enrichment can occur through the dynamics of nutrients such as magnesium and boron.}, }
@article {pmid36890125, year = {2023}, author = {Su, CC and Fung, JA and Chang, RJ and Chang, CJ and Jan, JF and Shih, HT and Chen, JC}, title = {TaqMan Quantitative-PCR Detection of Xylella taiwanensis in Taiwan.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-01-23-0064-RE}, pmid = {36890125}, issn = {0191-2917}, abstract = {Xylella taiwanensis (Xt) is a nutritionally fastidious bacterial pathogen causing pear leaf scorch disease (PLSD) in Taiwan. The disease causes early defoliation, loss of tree vigor and reduction in fruit yield and quality. No cure for PLSD is available. The only option for growers to control the disease is to use pathogen-free propagation material, which requires early and accurate detection of Xt. Currently, only one simplex PCR method is available for the diagnosis of PLSD. We developed five Xt-specific TaqMan quantitative PCR (TaqMan qPCR) systems (primers-probe sets) for detection of Xt. The PCR systems target three conserved genomic loci commonly used in bacterial pathogen detection: the 16S rRNA gene (rrs), the 16S-23S rRNA intergenic transcribed sequence (16S-23S rRNA ITS), and the DNA gyrase gene (gyrB). BLAST analysis using the GenBank nr sequence database, including whole genome sequences of 88 Xanthomonas campestris pv. campestris (Xcc) strains, 147 X. fastidiosa (Xf) strains, and 32 Xt strains, showed that all primer and probe sequences were specific only to Xt. Single nucleotide polymorphisms (SNPs) provided the primer/probe specificity to Xt. The PCR systems were evaluated by using DNA samples from pure cultures of two Xt strains, one Xf strain, one Xcc strain and 140 plant samples collected from 23 pear orchards in four counties in Taiwan. The two-copy rrs and 16S-23S rRNA ITS-based PCR systems (Xt803-F/R, Xt731-F/R, and Xt16S-F/R) showed higher detection sensitivity than the two single-copy gyrB-based systems (XtgB1-F/R and XtgB2-F/R). A metagenomic analysis of a representative PLSD leaf sample detected the presence of non-Xt proteobacteria and fungal pathogens that should be taken into consideration in PLSD, as they might interfere with diagnosis.}, }
@article {pmid36889461, year = {2023}, author = {Chen, H and Zheng, Y and Zhang, X and Liu, S and Yin, Y and Guo, Y and Wang, X and Zhang, Y and Zhao, C and Gai, W and Wang, H}, title = {Clinical evaluation of cell-free (cf) and cellular metagenomic next-generation sequencing of infected body fluids.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2023.02.018}, pmid = {36889461}, issn = {2090-1224}, abstract = {INTRODUCTION: Previous studies have evaluated metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) for pathogen detection in blood and body fluid samples. However, no study has assessed the diagnostic efficacy of mNGS using cellular DNA.<br><br>OBJECTIVES: This is the first study to systematically evaluate the efficacy of cfDNA and cellular DNA mNGS for pathogen detection.<br><br>METHODS: A panel of seven microorganisms was used to compare cfDNA and cellular DNA mNGS assays concerning limit of detection (LoD), linearity, robustness to interference, and precision. In total, 248 specimens were collected between December 2020 and December 2021. The medical records of all the patients were reviewed. These specimens were analysed using cfDNA and cellular DNA mNGS assays, and the mNGS results were confirmed using viral qPCR, 16S rRNA, and internal transcribed spacer (ITS) amplicon next-generation sequencing.<br><br>RESULTS: The LoD of cfDNA and cellular DNA mNGS was 9.3 to 149 genome equivalents (GE)/mL and 27 to 466 colony-forming units (CFU)/mL, respectively. The intra- and inter-assay reproducibility of cfDNA and cellular DNA mNGS was 100%. Clinical evaluation revealed that cfDNA mNGS was good at detecting the virus in blood samples (receiver operating characteristic (ROC) area under the curve (AUC), 0.9841). In contrast, the performance of cellular DNA mNGS was better than that of cfDNA mNGS in high host background samples. Overall, the diagnostic efficacy of cfDNA combined with cellular DNA mNGS (ROC AUC, 0.8583) was higher than that of cfDNA (ROC AUC, 0.8041) or cellular DNA alone (ROC AUC, 0.7545).<br><br>CONCLUSION: Overall, cfDNA mNGS is good for detecting viruses, and cellular DNA mNGS is suitable for high host background samples. The diagnostic efficacy was higher when cfDNA and cellular DNA mNGS were combined.}, }
@article {pmid36889095, year = {2023}, author = {Li, B and Tao, Y and Mao, Z and Gu, Q and Han, Y and Hu, B and Wang, H and Lai, A and Xing, P and Wu, QL}, title = {Iron oxides act as an alternative electron acceptor for aerobic methanotrophs in anoxic lake sediments.}, journal = {Water research}, volume = {234}, number = {}, pages = {119833}, doi = {10.1016/j.watres.2023.119833}, pmid = {36889095}, issn = {1879-2448}, abstract = {Conventional aerobic CH4-oxidizing bacteria (MOB) are frequently detected in anoxic environments, but their survival strategy and ecological contribution are still enigmatic. Here we explore the role of MOB in enrichment cultures under O2 gradients and an iron-rich lake sediment in situ by combining microbiological and geochemical techniques. We found that enriched MOB consortium used ferric oxides as alternative electron acceptors for oxidizing CH4 with the help of riboflavin when O2 was unavailable. Within the MOB consortium, MOB transformed CH4 to low molecular weight organic matter such as acetate for consortium bacteria as a carbon source, while the latter secrete riboflavin to facilitate extracellular electron transfer (EET). Iron reduction coupled to CH4 oxidation mediated by the MOB consortium was also demonstrated in situ, reducing 40.3% of the CH4 emission in the studied lake sediment. Our study indicates how MOBs survive under anoxia and expands the knowledge of this previously overlooked CH4 sink in iron-rich sediments.}, }
@article {pmid36888627, year = {2023}, author = {Leonard, MM and Kenyon, V and Valitutti, F and Pennacchio-Harrington, R and Piemontese, P and Francavilla, R and Norsa, L and Passaro, T and Crocco, M and Baldassarre, M and Trovato, CM and Fasano, A and , }, title = {Cohort profile: Celiac disease genomic, environmental, microbiome and metabolome study; a prospective longitudinal birth cohort study of children at-risk for celiac disease.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0282739}, doi = {10.1371/journal.pone.0282739}, pmid = {36888627}, issn = {1932-6203}, abstract = {The Celiac Disease Genomic, Environmental, Microbiome and Metabolomic (CDGEMM) study is an international prospective birth cohort in children at-risk of developing celiac disease (CD). The CDGEMM study has been designed to take a multi-omic approach to predicting CD onset in at-risk individuals. Participants are required to have a first-degree family member with biopsy diagnosed CD and must be enrolled prior to the introduction of solid food. Participation involves providing blood and stool samples longitudinally over a period of five years as well as answering questionnaires related to the participant, their family, and environment. Recruitment and data collection have been ongoing since 2014. As of 2022 we have a total of 554 participants and the average age of the cohort is 56.4 months. A total of 54 participants have developed positive antibodies for CD and 31 have confirmed CD. Approximately 80% of the 54 participants with CD have developed it by 3 years of age. To date we have identified several microbial strains, pathways, and metabolites occurring in increased abundance and detected before CD onset, which have previously been linked to autoimmune and inflammatory conditions while others occurred in decreased abundance before CD onset and are known to have anti-inflammatory effects. Our ongoing analysis includes expanding our metagenomic and metabolomic analyses, evaluating environmental risk factors linked to CD onset, and mechanistic studies investigating how alterations in the microbiome and metabolites may protect against or contribute to CD development.}, }
@article {pmid36882798, year = {2023}, author = {Inda-Díaz, JS and Lund, D and Parras-Moltó, M and Johnning, A and Bengtsson-Palme, J and Kristiansson, E}, title = {Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {44}, pmid = {36882798}, issn = {2049-2618}, abstract = {BACKGROUND: Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established in existing resistance gene databases. In contrast, the remaining latent ARGs are typically unknown and overlooked in most sequencing-based studies. Our view of the resistome and its diversity is therefore incomplete, which hampers our ability to assess risk for promotion and spread of yet undiscovered resistance determinants.<br><br>RESULTS: A reference database consisting of both established and latent ARGs (ARGs not present in current resistance gene repositories) was created. By analyzing more than 10,000 metagenomic samples, we showed that latent ARGs were more abundant and diverse than established ARGs in all studied environments, including the human- and animal-associated microbiomes. The pan-resistomes, i.e., all ARGs present in an environment, were heavily dominated by latent ARGs. In comparison, the core-resistome, i.e., ARGs that were commonly encountered, comprised both latent and established ARGs. We identified several latent ARGs shared between environments and/or present in human pathogens. Context analysis of these genes showed that they were located on mobile genetic elements, including conjugative elements. We, furthermore, identified that wastewater microbiomes had a surprisingly large pan- and core-resistome, which makes it a potentially high-risk environment for the mobilization and promotion of latent ARGs.<br><br>CONCLUSIONS: Our results show that latent ARGs are ubiquitously present in all environments and constitute a diverse reservoir from which new resistance determinants can be recruited to pathogens. Several latent ARGs already had high mobile potential and were present in human pathogens, suggesting that they may constitute emerging threats to human health. We conclude that the full resistome-including both latent and established ARGs-needs to be considered to properly assess the risks associated with antibiotic selection pressures. Video Abstract.}, }
@article {pmid36882742, year = {2023}, author = {Ji, Z and Ma, L}, title = {Controlling taxa abundance improves metatranscriptomics differential analysis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {60}, pmid = {36882742}, issn = {1471-2180}, support = {R01-GM135440/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: A common task in analyzing metatranscriptomics data is to identify microbial metabolic pathways with differential RNA abundances across multiple sample groups. With information from paired metagenomics data, some differential methods control for either DNA or taxa abundances to address their strong correlation with RNA abundance. However, it remains unknown if both factors need to be controlled for simultaneously.<br><br>RESULTS: We discovered that when either DNA or taxa abundance is controlled for, RNA abundance still has a strong partial correlation with the other factor. In both simulation studies and a real data analysis, we demonstrated that controlling for both DNA and taxa abundances leads to superior performance compared to only controlling for one factor.<br><br>CONCLUSIONS: To fully address the confounding effects in analyzing metatranscriptomics data, both DNA and taxa abundances need to be controlled for in the differential analysis.}, }
@article {pmid36882494, year = {2023}, author = {Dittmer, J and Bredon, M and Moumen, B and Raimond, M and Grève, P and Bouchon, D}, title = {The terrestrial isopod symbiont 'Candidatus Hepatincola porcellionum' is a potential nutrient scavenger related to Holosporales symbionts of protists.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {18}, pmid = {36882494}, issn = {2730-6151}, abstract = {The order Holosporales (Alphaproteobacteria) encompasses obligate intracellular bacterial symbionts of diverse Eukaryotes. These bacteria have highly streamlined genomes and can have negative fitness effects on the host. Herein, we present a comparative analysis of the first genome sequences of 'Ca. Hepatincola porcellionum', a facultative symbiont occurring extracellularly in the midgut glands of terrestrial isopods. Using a combination of long-read and short-read sequencing, we obtained the complete circular genomes of two Hepatincola strains and an additional metagenome-assembled draft genome. Phylogenomic analysis validated its phylogenetic position as an early-branching family-level clade relative to all other established Holosporales families associated with protists. A 16S rRNA gene survey revealed that this new family encompasses diverse bacteria associated with both marine and terrestrial host species, which expands the host range of Holosporales bacteria from protists to several phyla of the Ecdysozoa (Arthropoda and Priapulida). Hepatincola has a highly streamlined genome with reduced metabolic and biosynthetic capacities as well as a large repertoire of transmembrane transporters. This suggests that this symbiont is rather a nutrient scavenger than a nutrient provider for the host, likely benefitting from a nutrient-rich environment to import all necessary metabolites and precursors. Hepatincola further possesses a different set of bacterial secretion systems compared to protist-associated Holosporales, suggesting different host-symbiont interactions depending on the host organism.}, }
@article {pmid36882183, year = {2023}, author = {Wu, J and Liu, Q and Li, M and Xu, J and Wang, C and Zhang, J and Minfeng, X and Bin, Y and Xia, J}, title = {PhaGAA: an integrated web server platform for phage genome annotation and analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad120}, pmid = {36882183}, issn = {1367-4811}, abstract = {MOTIVATION: Phage genome annotation plays a key role in the design of phage therapy. To date, there have been various genome annotation tools for phages, but most of these tools focus on mono-functional annotation and have complex operational processes. Accordingly, comprehensive and user-friendly platforms for phage genome annotation are needed.<br><br>RESULTS: Here, we propose PhaGAA, an online integrated platform for phage genome annotation and analysis. By incorporating several annotation tools, PhaGAA is constructed to annotate prophage genome at DNA- and protein-levels and provide the analytical results. Furthermore, PhaGAA could mine and annotate phage genomes from bacterial genome or metagenome. In summary, PhaGAA will be a useful resource for experimental biologists, and help advance the phage synthetic biology in basic and application research.<br><br>AVAILABILITY: PhaGAA is freely available at http://phage.xialab.info/.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid36881655, year = {2023}, author = {Watanabe, M and Motooka, D and Yamasaki, S}, title = {The kinetics of signaling through the common FcRγ chain determine cytokine profiles in dendritic cells.}, journal = {Science signaling}, volume = {16}, number = {775}, pages = {eabn9909}, doi = {10.1126/scisignal.abn9909}, pmid = {36881655}, issn = {1937-9145}, abstract = {The common Fc receptor γ (FcRγ) chain is a signaling subunit common to several immune receptors, but cellular responses induced by FcRγ-coupled receptors are diverse. We investigated the mechanisms by which FcRγ generates divergent signals when coupled to Dectin-2 and Mincle, structurally similar C-type lectin receptors that induce the release of different cytokines from dendritic cells. Chronological tracing of transcriptomic and epigenetic changes upon stimulation revealed that Dectin-2 induced early and strong signaling, whereas Mincle-mediated signaling was delayed, which reflects their expression patterns. Generation of early and strong FcRγ-Syk signaling by engineered chimeric receptors was sufficient to recapitulate a Dectin-2-like gene expression profile. Early Syk signaling selectively stimulated the activity of the calcium ion-activated transcription factor NFAT, which rapidly altered the chromatin status and transcription of the Il2 gene. In contrast, proinflammatory cytokines, such as TNF, were induced regardless of FcRγ signaling kinetics. These results suggest that the strength and timing of FcRγ-Syk signaling can alter the quality of cellular responses through kinetics-sensing signaling machineries.}, }
@article {pmid36881114, year = {2023}, author = {Anju, VT and Busi, S and Mohan, MS and Salim, SA and Ar, S and Imchen, M and Kumavath, R and Dyavaiah, M and Prasad, R}, title = {Surveillance and mitigation of soil pollution through metagenomic approaches.}, journal = {Biotechnology &amp; genetic engineering reviews}, volume = {}, number = {}, pages = {1-34}, doi = {10.1080/02648725.2023.2186330}, pmid = {36881114}, issn = {2046-5556}, abstract = {Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.}, }
@article {pmid36879954, year = {2023}, author = {Wang, C and Hu, J and Gu, Y and Wang, X and Chen, Y and Yuan, W}, title = {Application of next-generation metagenomic sequencing in the diagnosis and treatment of acute spinal infections.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e13951}, pmid = {36879954}, issn = {2405-8440}, abstract = {OBJECTIVES: The purpose of this study was to verify the value of metagenomic next-generation sequencing (mNGS) in detecting the pathogens causing acute spinal infection by reviewing the results of mNGS in 114 patients.<br><br>METHODS: A total of 114 patients were included from our hospital. Samples (tissue/blood) were sent for mNGS detection, and the remaining samples were sent to the microbiology laboratory for pathogen culture, smear, histopathological analysis, and other tests. Patients' medical records were reviewed to determine their rates of detection, time needed, guidance for antibiotic treatment and clinical outcomes.<br><br>RESULTS: mNGS showed a satisfying diagnostic positive percent agreement of 84.91% (95% confidence interval (CI): 6.34%-96.7%), compared to 30.19% (95% CI: 21.85%-39.99%) for culture and 43.40% (95% CI: 31.39%-49.97%) for conventional methods (p&#xa0;<&#xa0;0.0125), and mNGS was found positive in 46 culture and smear negative samples. The time required for pathogen identification using mNGS ranged from 29&#xa0;h to 53&#xa0;h, which showed an advantage over culture (90.88&#xa0;&#xb1;&#xa0;8.33&#xa0;h; P&#xa0;<&#xa0;0.05). mNGS also played an important role in optimizing antibiotic regimens in patients with negative results obtained using conventional methods. The treatment success rate (TSR) of patients using mNGS-guided antibiotic regimens (20/24, 83.33%) was significantly higher than that of patients using empirical antibiotics (13/23, 56.52%) (P&#xa0;<&#xa0;0.0001).<br><br>CONCLUSIONS: mNGS shows promising potential in the pathogenic diagnosis of acute spinal infections and may enable clinicians to make more timely and effective adjustments to antibiotic regimens.}, }
@article {pmid36879851, year = {2023}, author = {Yu, Y and Wang, S and Dong, G and Niu, Y}, title = {Diagnostic Performance of Metagenomic Next⁃Generation Sequencing in the Diagnosis of Prosthetic Joint Infection Using Tissue Specimens.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {1193-1201}, pmid = {36879851}, issn = {1178-6973}, abstract = {PURPOSE: The purpose of this study was to evaluate the ability of metagenomic next-generation sequencing (mNGS) diagnosing prosthetic joint infection (PJI) using tissue from hip/knee rapidly and precisely, especially in patients who had received antibiotic treatment within the preceding two weeks.<br><br>METHODS: From May 2020 to March 2022, 52 cases with suspected PJI were enrolled. mNGS was performed on surgical tissue samples. The sensitivity and specificity of mNGS in diagnosis was evaluated using culture in conjunction with MSIS criteria. This study also looked at how antibiotic use affected culture and mNGS efficacy.<br><br>RESULTS: According to MSIS criteria, 31 of the 44 cases had PJI, and 13 were classified in the aseptic loosening group. Sensitivity, specificity, positive/negative predictive value (PPV/NPV), positive/negative likelihood ratio (PLR/NLR), and area under the curve (AUC) of mNGS assay were 80.6% (71.9-91.8%), 84.6 (73.7-97.9%), 92.6 (84.2-98.7%), 64.7 (58.6-74.7%), 5.241 (4.081-6.693), 0.229 (0.108-0.482) and 0.826 (0.786-0.967), respectively, with MSIS as a reference. When MSIS was used as a reference, the results of culture assay were 45.2% (40.8-51.5%), 100 (100.0-100.0%), 100 (100.0-100.0%), 43.3 (39.1-49.5%), +&#x221e;, 0.548 (0.396-0.617) and 0.726 (0.621-0.864), respectively. The AUC values for mNGS and culture were 0.826 and 0.731, respectively, and the differences were insignificant. mNGS demonstrated higher sensitivity than culture in PJI subjects who had previously received antibiotic treatment within 2 weeks (69.5% vs 23.1%, P =&#xa0;0.03).<br><br>CONCLUSION: In our series, mNGS yield a higher sensitivity for diagnosis and pathogen detection of PJI compared to microbiological culture. Additionally, mNGS is less affected by prior antibiotic exposure.}, }
@article {pmid36879645, year = {2023}, author = {Feng, L and Chen, J and Luo, Q and Su, M and Chen, P and Lai, R and Shen, C and Zhou, H and Wang, H and Sun, X and Chen, L and Xia, H and Feng, H}, title = {mNGS facilitates the accurate diagnosis and antibiotic treatment of suspicious critical CNS infection in real practice: A retrospective study.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220578}, pmid = {36879645}, issn = {2391-5412}, abstract = {Whether metagenomic next-generation sequencing (mNGS) could benefit patients with suspected severe central nervous system (CNS) infection in terms of diagnosis and antibiotic treatment remains unknown. We retrospectively analyzed 79 patients with suspected CNS infection and undertook mNGS. The value of mNGS was investigated in terms of identification of pathogen and guidance for the adjustment of antibiotic treatment. The relationship between the time of initiating mNGS since onset and the Glasgow Outcome Scale (GOS) score after 90-day follow-up were analyzed. Fifty out of 79 cases with suspicious severe CNS infection were finally diagnosed. Despite previous routine laboratory tests, mNGS further promoted the accurate identification of pathogens in 23 cases (47.9%). The sensitivity, specificity, and accuracy of mNGS test in this study were 84.0, 79.3, and 82.3%, respectively. Furthermore, mNGS facilitated the adjustment of empirical antibiotic treatments in 38 cases (48.1%). The time of taking mNGS since onset had an insignificant weak positive correlation with GOS after 90-day follow-up (r = -0.73, P = 0.08). mNGS facilitated the accurate identification of pathogens in suspicious severe CNS infections and promoted the accurate antibiotic therapy even empirical antibiotics were administrated. It should be taken as early as possible to improve the clinical outcome of patients with suspicious severe CNS infection.}, }
@article {pmid36879606, year = {2023}, author = {Duncan, A and Barry, K and Daum, C and Eloe-Fadrosh, E and Roux, S and Schmidt, K and Tringe, SG and Valentin, KU and Varghese, N and Salamov, A and Grigoriev, IV and Leggett, RM and Moulton, V and Mock, T}, title = {Dataset of 143 metagenome-assembled genomes from the Arctic and Atlantic Oceans, including 21 for eukaryotic organisms.}, journal = {Data in brief}, volume = {47}, number = {}, pages = {108990}, pmid = {36879606}, issn = {2352-3409}, abstract = {This article presents metagenome-assembled genomes (MAGs) for both eukaryotic and prokaryotic organisms originating from the Arctic and Atlantic oceans, along with gene prediction and functional annotation for MAGs from both domains. Eleven samples from the chlorophyll-a maximum layer of the surface ocean were collected during two cruises in 2012; six from the Arctic in June-July on ARK-XXVII/1 (PS80), and five from the Atlantic in November on ANT-XXIX/1 (PS81). Sequencing and assembly was carried out by the Joint Genome Institute (JGI), who provide annotation of the assembled sequences, and 122 MAGs for prokaryotic organisms. A subsequent binning process identified 21 MAGs for eukaryotic organisms, mostly identified as Mamiellophyceae or Bacillariophyceae. The data for each MAG includes sequences in FASTA format, and tables of functional annotation of genes. For eukaryotic MAGs, transcript and protein sequences for predicted genes are available. A spreadsheet is provided summarising quality measures and taxonomic classifications for each MAG. These data provide draft genomes for uncultured marine microbes, including some of the first MAGs for polar eukaryotes, and can provide reference genetic data for these environments, or used in genomics-based comparison between environments.}, }
@article {pmid36879349, year = {2023}, author = {Li, Z and Zhao, X and Jian, L and Wang, B and Luo, H}, title = {Rumen microbial-driven metabolite from grazing lambs potentially regulates body fatty acid metabolism by lipid-related genes in liver.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {39}, pmid = {36879349}, issn = {1674-9782}, abstract = {BACKGROUND: Lipid metabolism differs significantly between grazing and stall-feeding lambs, affecting the quality of livestock products. As two critical organs of lipid metabolism, the differences between feeding patterns on rumen and liver metabolism remain unclear. In this study, 16S rRNA, metagenomics, transcriptomics, and untargeted metabolomics were utilized to investigate the key rumen microorganisms and metabolites, as well as liver genes and metabolites associated with fatty acid metabolism under indoor feeding (F) and grazing (G).<br><br>RESULTS: Compared with grazing, indoor feeding increased ruminal propionate content. Using metagenome sequencing in combination with 16S rRNA amplicon sequencing, the results showed that&#xa0;the abundance of propionate-producing Succiniclasticum and hydrogenating bacteria Tenericutes was enriched in the F group. For rumen metabolism, grazing caused up-regulation of EPA, DHA and oleic acid and down-regulation of decanoic acid, as well as, screening for 2-ketobutyric acid as a vital differential metabolite, which was enriched in the propionate metabolism pathway. In the liver, indoor feeding increased 3-hydroxypropanoate and citric acid content, causing changes in propionate metabolism and citrate cycle, while decreasing the ETA content. Then, the liver transcriptome revealed that 11 lipid-related genes were differentially expressed in the two feeding patterns. Correlation analysis showed that the expression of CYP4A6, FADS1, FADS2, ALDH6A1 and CYP2C23 was significantly associated with the propionate metabolism process, suggesting that propionate metabolism may be an important factor mediating the hepatic lipid metabolism. Besides, the unsaturated fatty acids in muscle, rumen and liver also had a close correlation.<br><br>CONCLUSIONS: Overall, our data demonstrated that rumen microbial-driven metabolite from grazing lambs potentially regulates multiple hepatic lipid-related genes, ultimately affecting body fatty acid metabolism.}, }
@article {pmid36879316, year = {2023}, author = {Korry, BJ and Belenky, P}, title = {Trophic level and proteobacteria abundance drive antibiotic resistance levels in fish from coastal New England.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {16}, pmid = {36879316}, issn = {2524-4671}, support = {R01DK125382/NH/NIH HHS/United States ; R01DK125382/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: The natural marine environment represents a vast reservoir of antimicrobial resistant bacteria. The wildlife that inhabits this environment plays an important role as the host to these bacteria and in the dissemination of resistance. The relationship between host diet, phylogeny, and trophic level and the microbiome/resistome in marine fish is not fully understood. To further explore this relationship, we utilize shotgun metagenomic sequencing to define the gastrointestinal tract microbiomes of seven different marine vertebrates collected in coastal New England waters.<br><br>RESULTS: We identify inter and intraspecies differences in the gut microbiota of these wild marine fish populations. Furthermore, we find an association between antibiotic resistance genes and host dietary guild, which suggests that higher trophic level organisms have a greater abundance of resistance genes. Additionally, we demonstrate that antibiotic resistance gene burden is positively correlated with Proteobacteria abundance in the microbiome. Lastly, we identify dietary signatures within the gut of these fish and find evidence of possible dietary selection for bacteria with specific carbohydrate utilization potential.<br><br>CONCLUSIONS: This work establishes a link between host lifestyle/dietary guild, and microbiome composition and the abundance of antibiotic resistance genes within the gastrointestinal tract of marine organisms. We expand the current understanding of marine organism-associated microbial communities and their role as reservoirs of antimicrobial resistance genes.}, }
@article {pmid36879274, year = {2023}, author = {Lousada, MB and Edelkamp, J and Lachnit, T and Fehrholz, M and Jimenez, F and Paus, R}, title = {Laser capture microdissection as a method for investigating the human hair follicle microbiome reveals region-specific differences in the bacteriome profile.}, journal = {BMC research notes}, volume = {16}, number = {1}, pages = {29}, pmid = {36879274}, issn = {1756-0500}, abstract = {OBJECTIVE: Human hair follicles (HFs) are populated by a rich and diverse microbiome, traditionally evaluated by methods that inadvertently sample the skin microbiome and/or miss microbiota located in deeper HF regions. Thereby, these methods capture the human HF microbiome in a skewed and incomplete manner. This pilot study aimed to use laser-capture microdissection of human scalp HFs, coupled with 16S rRNA gene sequencing to sample the HF microbiome and overcome these methodological limitations.<br><br>RESULTS: HFs were laser-capture microdissected (LCM) into three anatomically distinct regions. All main known core HF bacterial colonisers, including Cutibacterium, Corynebacterium and Staphylococcus, were identified, in all three HF regions. Interestingly, region-specific variations in &#x3b1;-diversity and microbial abundance of the core microbiome genera and Reyranella were identified, suggestive of variations in microbiologically relevant microenvironment characteristics. This pilot study therefore shows that LCM-coupled with metagenomics is a powerful tool for analysing the microbiome of defined biological niches. Refining and complementing this method with broader metagenomic techniques will facilitate the mapping of dysbiotic events associated with HF diseases and targeted therapeutic interventions.}, }
@article {pmid36878288, year = {2023}, author = {Chai, X and Wen, L and Song, Y and He, X and Yue, J and Wu, J and Chen, X and Cai, Z and Qi, Z}, title = {DEHP exposure elevated cardiovascular risk in obese mice by disturbing the arachidonic acid metabolism of gut microbiota.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {162615}, doi = {10.1016/j.scitotenv.2023.162615}, pmid = {36878288}, issn = {1879-1026}, abstract = {Phthalate esters (PAEs) are one of the significant classes of emerging contaminants that are increasingly detected in environmental and human samples. Nevertheless, the current toxicity studies rarely report how PAEs affect the cardiovascular system, especially in obese individuals. In this study, diet-induced obese mice and corresponding normal mice were exposed to di(2-ethylhexyl) phthalate (DEHP) by oral gavage at environmentally relevant concentrations and key characteristics of cardiovascular risk were examined. The 16S rRNA and high-resolution mass spectrometry were used to investigate the alterations in the gut microbial profile and metabolic homeostasis. The results indicated that the cardiovascular system of fat individuals was more susceptible to DEHP exposure than mice in the lean group. 16S rRNA-based profiling and correlation analysis collectively suggested DEHP-induced gut microbial remodeling in fed a high-fat diet mice, represented by the abundance of the genus Faecalibaculum. Using metagenomic approaches, Faecalibaculum rodentium was identified as the top-ranked candidate bacterium. Additionally, metabolomics data revealed that DEHP exposure altered the gut metabolic homeostasis of arachidonic acid (AA), which is associated with adverse cardiovascular events. Finally, cultures of Faecalibaculum rodentium were treated with AA in vitro to verify the role of Faecalibaculum rodentium in altering AA metabolism. Our findings provide novel insights into DEHP exposure induced cardiovascular damage in obese individuals and suggest that AA could be used as a potential modulator of gut microbiota to prevent related diseases.}, }
@article {pmid36790822, year = {2023}, author = {Kirsch-Gerweck, B and Bohnenkämper, L and Henrichs, MT and Alanko, JN and Bannai, H and Cazaux, B and Peterlongo, P and Burger, J and Stoye, J and Diekmann, Y}, title = {HaploBlocks: Efficient Detection of Positive Selection in Large Population Genomic Datasets.}, journal = {Molecular biology and evolution}, volume = {40}, number = {3}, pages = {}, pmid = {36790822}, issn = {1537-1719}, mesh = {*Genetics, Population ; *Metagenomics ; Genomics ; Genome ; Haplotypes ; }, abstract = {Genomic regions under positive selection harbor variation linked for example to adaptation. Most tools for detecting positively selected variants have computational resource requirements rendering them impractical on population genomic datasets with hundreds of thousands of individuals or more. We have developed and implemented an efficient haplotype-based approach able to scan large datasets and accurately detect positive selection. We achieve this by combining a pattern matching approach based on the positional Burrows-Wheeler transform with model-based inference which only requires the evaluation of closed-form expressions. We evaluate our approach with simulations, and find it to be both sensitive and specific. The computational resource requirements quantified using UK Biobank data indicate that our implementation is scalable to population genomic datasets with millions of individuals. Our approach may serve as an algorithmic blueprint for the era of "big data" genomics: a combinatorial core coupled with statistical inference in closed form.}, }
@article {pmid36377253, year = {2023}, author = {Tello, D and Gonzalez-Garcia, LN and Gomez, J and Zuluaga-Monares, JC and Garcia, R and Angel, R and Mahecha, D and Duarte, E and Leon, MDR and Reyes, F and Escobar-Velásquez, C and Linares-Vásquez, M and Cardozo, N and Duitama, J}, title = {NGSEP 4: Efficient and accurate identification of orthogroups and whole-genome alignment.}, journal = {Molecular ecology resources}, volume = {23}, number = {3}, pages = {712-724}, doi = {10.1111/1755-0998.13737}, pmid = {36377253}, issn = {1755-0998}, mesh = {*Software ; *Genome ; Genomics/methods ; Algorithms ; Metagenomics ; }, abstract = {Whole-genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment. Our results showed that the NGSEP algorithm for orthogroups identification has competitive accuracy and efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. NGSEP 4 also includes a new graphical user interface based on the JavaFX technology. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics.}, }
@article {pmid36877076, year = {2023}, author = {Kim, JE and Nam, H and Park, JI and Cho, H and Lee, J and Kim, HE and Kim, DK and Joo, KW and Kim, YS and Kim, BS and Park, S and Lee, H}, title = {Gut Microbial Genes and Metabolism for Methionine and Branched-Chain Amino Acids in Diabetic Nephropathy.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0234422}, doi = {10.1128/spectrum.02344-22}, pmid = {36877076}, issn = {2165-0497}, abstract = {Diabetic mellitus nephropathy (DMN) is a serious complication of diabetes and a major health concern. Although the pathophysiology of diabetes mellitus (DM) leading to DMN is uncertain, recent evidence suggests the involvement of the gut microbiome. This study aimed to determine the relationships among gut microbial species, genes, and metabolites in DMN through an integrated clinical, taxonomic, genomic, and metabolomic analysis. Whole-metagenome shotgun sequencing and nuclear magnetic resonance metabolomic analyses were performed on stool samples from 15 patients with DMN and 22 healthy controls. Six bacterial species were identified to be significantly elevated in the DMN patients after adjusting for age, sex, body mass index, and estimated glomerular filtration rate (eGFR). Multivariate analysis found 216 microbial genes and 6 metabolites (higher valine, isoleucine, methionine, valerate, and phenylacetate levels in the DMN group and higher acetate levels in the control group) that were differentially present between the DMN and control groups. Integrated analysis of all of these parameters and clinical data using the random-forest model showed that methionine and branched-chain amino acids (BCAAs) were among the most significant features, next to the eGFR and proteinuria, in differentiating the DMN group from the control group. Metabolic pathway gene analysis of BCAAs and methionine also revealed that many genes involved in the biosynthesis of these metabolites were elevated in the six species that were more abundant in the DMN group. The suggested correlation among taxonomic, genetic, and metabolic features of the gut microbiome would expand our understanding of gut microbial involvement in the pathogenesis of DMN and may provide potential therapeutic targets for DMN. IMPORTANCE Whole metagenomic sequencing uncovered specific members of the gut microbiota associated with DMN. The gene families derived from the discovered species are involved in the metabolic pathways of methionine and branched-chain amino acids. Metabolomic analysis using stool samples showed increased methionine and branched-chain amino acids in DMN. These integrative omics results provide evidence of the gut microbiota-associated pathophysiology of DMN, which can be further studied for disease-modulating effects via prebiotics or probiotics.}, }
@article {pmid36877067, year = {2023}, author = {Ong, DRY and Gutiérrez-Rodríguez, A and Garczarek, L and Marie, D and Lopes Dos Santos, A}, title = {Nested PCR Approach for petB Gene Metabarcoding of Marine Synechococcus Populations.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0408622}, doi = {10.1128/spectrum.04086-22}, pmid = {36877067}, issn = {2165-0497}, abstract = {The molecular diversity of marine picocyanobacterial populations, an important component of phytoplankton communities, is better characterized using high-resolution marker genes than the 16S rRNA gene as they have greater sequence divergence to differentiate between closely related picocyanobacteria groups. Although specific ribosomal primers have been developed, another general disadvantage of bacterial ribosome-based diversity analyses is the variable number of rRNA gene copies. To overcome these issues, the single-copy petB gene, encoding the cytochrome b6 subunit of the cytochrome b6f complex, has been used as a high-resolution marker gene to characterize Synechococcus diversity. We have designed new primers targeting the petB gene and proposed a nested PCR method (termed Ong_2022) for metabarcoding of marine Synechococcus populations obtained by flow cytometry cell sorting. We evaluated the specificity and sensitivity of Ong_2022 against the standard amplification protocol (termed Mazard_2012) using filtered seawater samples. The Ong_2022 approach was also tested on flow cytometry-sorted Synechococcus populations. Samples (filtered and sorted) were obtained in the Southwest Pacific Ocean, from subtropical (ST) and subantarctic (SA) water masses. The two PCR approaches using filtered samples recovered the same dominant subclades, Ia, Ib, IVa, and IVb, with small differences in relative abundance across the distinct samples. For example, subclade IVa was dominant in ST samples with the Mazard_2012 approach, while the same samples processed with Ong_2022 showed similar contributions of subclades IVa and Ib to the total community. The Ong_2022 approach generally captured a higher genetic diversity of Synechococcus subcluster 5.1 than the Mazard_2012 approach while having a lower proportion of incorrectly assigned amplicon sequence variants (ASVs). All flow cytometry-sorted Synechococcus samples could be amplified only by our nested approach. The taxonomic diversity obtained with our primers on both sample types was in agreement with the clade distribution observed by previous studies that applied other marker genes or PCR-free metagenomic approaches under similar environmental conditions. IMPORTANCE The petB gene has been proposed as a high-resolution marker gene to access the diversity of marine Synechococcus populations. A systematic metabarcoding approach based on the petB gene would improve the characterization/assessment of the Synechococcus community structure in marine planktonic ecosystems. We have designed and tested specific primers to be applied in a nested PCR protocol (Ong_2022) for metabarcoding the petB gene. The Ong_2022 protocol can be applied to samples with low DNA content, such as those obtained by flow cytometry cell sorting, allowing the simultaneous assessment of the genetic diversity of Synechococcus populations and cellular properties and activities (e.g., nutrient cell ratios or carbon uptake rates). Our approach will allow future studies using flow cytometry to investigate the link between ecological traits and taxonomic diversity of marine Synechococcus.}, }
@article {pmid36877031, year = {2023}, author = {Barnett, SE and Egan, R and Foster, B and Eloe-Fadrosh, EA and Buckley, DH}, title = {Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing.}, journal = {mBio}, volume = {}, number = {}, pages = {e0358422}, doi = {10.1128/mbio.03584-22}, pmid = {36877031}, issn = {2150-7511}, abstract = {Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.}, }
@article {pmid36876113, year = {2023}, author = {Anderson, BD and Bisanz, JE}, title = {Challenges and opportunities of strain diversity in gut microbiome research.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1117122}, pmid = {36876113}, issn = {1664-302X}, abstract = {Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than de novo mutations. As such, the conserved portion of the genome is often a fraction of the pangenome which gives rise to significant phenotypic variation, particularly in traits which are important in host microbe interactions. In this review, we discuss the mechanisms that give rise to strain variation and methods that can be used to study it. We identify that while strain diversity can act as a major barrier in interpreting and generalizing microbiome data, it can also be a powerful tool for mechanistic research. We then highlight recent examples demonstrating the importance of strain variation in colonization, virulence, and xenobiotic metabolism. Moving past taxonomy and the species concept will be crucial for future mechanistic research to understand microbiome structure and function.}, }
@article {pmid36876106, year = {2023}, author = {Zhang, K and Zhang, Y and Deng, M and Wang, P and Yue, X and Wang, P and Li, W}, title = {Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1125709}, pmid = {36876106}, issn = {1664-302X}, abstract = {INTRODUCTION: The expanded granular sludge bed (EGSB) is a major form of anaerobic digestion system during wastewater treatment. Yet, the dynamics of microbial and viral communities and members functioning in nitrogen cycling along with monthly changing physicochemical properties have not been well elucidated.<br><br>METHODS: Here, by collecting the anaerobic activated sludge samples from a continuously operating industrial-scale EGSB reactor, we conducted 16S rRNA gene amplicon sequencing and metagenome sequencing to reveal the microbial community structure and variation with the ever-changing physicochemical properties along within a year.<br><br>RESULTS: We observed a clear monthly variation of microbial community structures, while COD, the ratio of volatile suspended solids (VSS) to total suspended solids (TSS) (VSS/TSS ratio), and temperature were predominant factors in shaping community dissimilarities examined by generalized boosted regression modeling (GBM) analysis. Meanwhile, a significant correlation was found between the changing physicochemical properties and microbial communities (p&#x2009;<0.05). The alpha diversity (Chao1 and Shannon) was significantly higher (p&#x2009;<0.05) in both winter (December, January, and February) and autumn (September, October, and November) with higher organic loading rate (OLR), higher VSS/TSS ratio, and lower temperature, resulting higher biogas production and nutrition removal efficiency. Further, 18 key genes covering nitrate reduction, denitrification, nitrification, and nitrogen fixation pathways were discovered, the total abundance of which was significantly associated with the changing environmental factors (p&#x2009;<0.05). Among these pathways, the dissimilatory nitrate reduction to ammonia (DNRA) and denitrification had the higher abundance contributed by the top highly abundant genes narGH, nrfABCDH, and hcp. The COD, OLR, and temperature were primary factors in affecting DNRA and denitrification by GBM evaluation. Moreover, by metagenome binning, we found the DNRA populations mainly belonged to Proteobacteria, Planctomycetota, and Nitrospirae, while the denitrifying bacteria with complete denitrification performance were all Proteobacteria. Besides, we detected 3,360 non-redundant viral sequences with great novelty, in which Siphoviridae, Podoviridae, and Myoviridae were dominant viral families. Interestingly, viral communities likewise depicted clear monthly variation and had significant associations with the recovered populations (p&#x2009;<0.05).<br><br>DISCUSSION: Our work highlights the monthly variation of microbial and viral communities during the continuous operation of EGSB affected by the predominant changing COD, OLR, and temperature, while DNRA and denitrification pathways dominated in this anaerobic system. The results also provide a theoretical basis for the optimization of the engineered system.}, }
@article {pmid36876103, year = {2023}, author = {Wang, L and Zhu, ZB and Zhang, L and Li, J and Zhao, Q}, title = {Editorial: Untangle the broad connections and tight interactions between human microbiota and complex diseases through data-driven approaches.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1157579}, pmid = {36876103}, issn = {1664-302X}, }
@article {pmid36876097, year = {2023}, author = {Farjana, N and Tu, Z and Furukawa, H and Yumoto, I}, title = {Environmental factors contributing to the convergence of bacterial community structure during indigo reduction.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1097595}, pmid = {36876097}, issn = {1664-302X}, abstract = {Indigo is solubilized through the reducing action of the microbiota that occurs during alkaline fermentation of composted leaves of Polygonum tinctorium L. (sukumo). However, the environmental effects on the microbiota during this treatment, as well as the mechanisms underlying the microbial succession toward stable state remain unknown. In this study, physicochemical analyses and Illumina metagenomic sequencing was used to determine the impact pretreatment conditions on the subsequent initiation of bacterial community transition and their convergence, dyeing capacity and the environmental factors critical for indigo reducing state during aging of sukumo. The initial pretreatment conditions analyzed included 60°C tap water (heat treatment: batch 1), 25°C tap water (control; batch 2), 25°C wood ash extract (high pH; batch 3) and hot wood ash extract (heat and high pH; batch 4), coupled with successive addition of wheat bran from days 5 to 194. High pH had larger impact than heat treatment on the microbiota, producing more rapid transitional changes from days 1 to 2. Although the initial bacterial community composition and dyeing intensity differed during days 2-5, the microbiota appropriately converged to facilitate indigo reduction from day 7 in all the batches, with Alkaliphilus oremalandii, Amphibacillus, Alkalicella caledoniensis, Atopostipes suicloalis and Tissierellaceae core taxa contributing to the improvement of when the dyeing intensity. This convergence is attributed to the continuous maintenance of high pH (day 1 ~) and low redox potential (day 2~), along with the introduction of wheat bran at day 5 (day 5~). PICRUSt2 predictive function profiling revealed the enrichment of phosphotransferease system (PTS) and starch and sucrose metabolism subpathways key toward indigo reduction. Seven NAD(P)-dependent oxidoreductases KEGG orthologs correlating to the dyeing intensity was also identified, with Alkalihalobacillus macyae, Alkalicella caledoniensis, and Atopostipes suicloalis contributing significantly toward the initiation of indigo reduction in batch 3. During the ripening period, the staining intensity was maintained by continuous addition of wheat bran and the successive emergence of indigo-reducing bacteria that also contributed to material circulation in the system. The above results provide insight into the interaction of microbial system and environmental factors in sukumo fermentation.}, }
@article {pmid36876060, year = {2023}, author = {Klair, D and Dobhal, S and Ahmad, A and Hassan, ZU and Uyeda, J and Silva, J and Wang, KH and Kim, S and Alvarez, AM and Arif, M}, title = {Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1039292}, pmid = {36876060}, issn = {1664-302X}, abstract = {Irrigation water is a common source of contamination that carries plant and foodborne human pathogens and provides a niche for proliferation and survival of microbes in agricultural settings. Bacterial communities and their functions in irrigation water were investigated by analyzing samples from wetland taro farms on Oahu, Hawaii using different DNA sequencing platforms. Irrigation water samples (stream, spring, and storage tank water) were collected from North, East, and West sides of Oahu and subjected to high quality DNA isolation, library preparation and sequencing of the V3-V4 region, full length 16S rRNA, and shotgun metagenome sequencing using Illumina iSeq100, Oxford Nanopore MinION and Illumina NovaSeq, respectively. Illumina reads provided the most comprehensive taxonomic classification at the phylum level where Proteobacteria was identified as the most abundant phylum in the stream source and associated water samples from wetland taro fields. Cyanobacteria was also a dominant phylum in samples from tank and spring water, whereas Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, over 50% of the valid short amplicon reads remained unclassified and inconclusive at the species level. In contrast, Oxford Nanopore MinION was a better choice for microbe classification at the genus and species levels as indicated by samples sequenced for full length 16S rRNA. No reliable taxonomic classification results were obtained while using shotgun metagenome data. In functional analyzes, only 12% of the genes were shared by two consortia and 95 antibiotic resistant genes (ARGs) were detected with variable relative abundance. Full descriptions of microbial communities and their functions are essential for the development of better water management strategies aimed to produce safer fresh produce and to protect plant, animal, human and environmental health. Quantitative comparisons illustrated the importance of selecting the appropriate analytical method depending on the level of taxonomic delineation sought in each microbiome.}, }
@article {pmid36875992, year = {2022}, author = {Tadrent, N and Dedeine, F and Hervé, V}, title = {SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes.}, journal = {F1000Research}, volume = {11}, number = {}, pages = {1522}, pmid = {36875992}, issn = {2046-1402}, abstract = {Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.}, }
@article {pmid36875536, year = {2022}, author = {Wahla, AQ and Anwar, S and Fareed, MI and Ikram, W and Ali, L and Alharby, HF and Bamagoos, AA and Almaghamsi, AA and Iqbal, S and Ali, S}, title = {Immobilization of metribuzin-degrading bacteria on biochar: Enhanced soil remediation and bacterial community restoration.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1027284}, pmid = {36875536}, issn = {1664-302X}, abstract = {Metribuzin (MB), a triazinone herbicide is extensively sprayed for weed control in agriculture, has been reported to contaminate soil, groundwater, and surface waters. In soil, MB residues can negatively affect not only the germination of subsequent crops but also disturb soil bacterial community. The present study describes the use of biochar as a carrier material to immobilize MB-degrading bacterial consortium, for remediation of MB-contaminated soil and restoration of soil bacterial community in soil microcosms. The bacterial consortium (MB3R) comprised four bacterial strains, i.e., Rhodococcus rhodochrous AQ1, Bacillus tequilensis AQ2, Bacillus aryabhattai AQ3, and Bacillus safensis AQ4. Significantly higher MB remediation was observed in soil augmented with bacterial consortium immobilized on biochar compared to the soil augmented with un-immobilized bacterial consortium. Immobilization of MB3R on biochar resulted in higher MB degradation rate (0.017 Kd[-1]) and reduced half-life (40 days) compared to 0.010 Kd[-1] degradation rate and 68 day half-life in treatments where un-immobilized bacterial consortium was employed. It is worth mentioning that the MB degradation products metribuzin-desamino (DA), metribuzin-diketo (DK), and metribuzin desamino-diketo (DADK) were detected in the treatments where MB3R was inoculated either alone or in combination with biochar. MB contamination significantly altered the composition of soil bacteria. However, soil bacterial community was conserved in response to augmentation with MB3R immobilized on biochar. Immobilization of the bacterial consortium MB3R on biochar can potentially be exploited for remediation of MB-contaminated soil and protecting its microbiota.}, }
@article {pmid36875219, year = {2023}, author = {Shamsuri, QS and Ab Majid, AH}, title = {Metagenomic 16S rRNA amplicon data of gut microbial diversity in three species of subterranean termites (Coptotermes gestroi, Globitermes sulphureus and Macrotermes gilvus).}, journal = {Data in brief}, volume = {47}, number = {}, pages = {108993}, pmid = {36875219}, issn = {2352-3409}, abstract = {In this paper, we present the metagenomic dataset of gut microbial DNA of the lower group of subterranean termites, i.e. Coptotermes gestroi, and the higher groups, i.e. Globitermes sulphureus and Macrotermes gilvus, in Penang, Malaysia. Two replicates of each species were sequenced using Next-Generation Sequencing (Illumina MiSeq) and analysed via QIIME2. The results returned with 210,248 sequences in C. gestroi, 224,972 in G. sulphureus, and 249,549 in M. gilvus. The sequence data were deposited in the NCBI Sequence Read Archive (SRA) under BioProject number of PRJNA896747. The community analysis showed that Bacteroidota is the most abundant phylum in C. gestroi and M. gilvus, while Spirochaetota is prevalent in G. sulphureus.}, }
@article {pmid36875193, year = {2023}, author = {Abdullah, B and Idorus, MY and Daud, S and Aazmi, S and Pillai, TK and Zain, ZM}, title = {Gut Microbiota Composition in the First and Third Trimester of Pregnancy among Malay Women is Associated with Body Mass Index: A Pilot Study.}, journal = {The Malaysian journal of medical sciences : MJMS}, volume = {30}, number = {1}, pages = {116-128}, pmid = {36875193}, issn = {1394-195X}, abstract = {BACKGROUND: This study has analysed the pattern of gut microbiota during the first and third trimesters among pregnant Malay women.<br><br>METHODS: This was a pilot prospective observational study involving 12 pregnant Malay women without any endocrine disorders and on neither antibiotics nor probiotics. Demographic details and anthropometric measurements were obtained, and the faecal 16S ribosomal ribonucleic acid (rRNA) metagenome microbiota of the first and third trimesters (T1 and T3) were analysed. Univariate and multivariate statistics, partial least squares discriminant analysis (PLSDA) and Kendall rank correlation testing were used to identify key genera and associations with pregnancy trimester and body mass index (BMI).<br><br>RESULTS: The most abundant phyla were Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria, with significant differences in composition at the genus level demonstrated between T1 and T3. Sequencing showed a statistically significant difference in beta diversity between normal and abnormal BMI at all taxonomic ranks (R [2] = 0.60; Q [2] = 0.23) and genus levels (R [2] = 0.57; Q [2] = 0.37). The relative abundances of Akkermansia (P < 0.05; false discovery rate [FDR] < 0.05), Olsenella (P < 0.05; FDR < 0.05) and Oscillospira (P < 0.05; FDR < 0.05) were found to be significantly higher in normal BMI cases by 2.4, 3.4 and 3.1 times, respectively.<br><br>CONCLUSION: Three genera (Akkermansia, Olsenella and Oscillospira) were correlated with normal BMI during pregnancy. All three could be promising biotherapeutic targets in body weight regulation during pregnancy, subsequently reducing complications associated with higher BMI.}, }
@article {pmid36875075, year = {2023}, author = {Xu, XJ and Lang, JD and Yang, J and Long, B and Liu, XD and Zeng, XF and Tian, G and You, X}, title = {Differences of gut microbiota and behavioral symptoms between two subgroups of autistic children based on γδT cells-derived IFN-γ Levels: A preliminary study.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1100816}, pmid = {36875075}, issn = {1664-3224}, abstract = {BACKGROUND: Autism Spectrum Disorders (ASD) are defined as a group of pervasive neurodevelopmental disorders, and the heterogeneity in the symptomology and etiology of ASD has long been recognized. Altered immune function and gut microbiota have been found in ASD populations. Immune dysfunction has been hypothesized to involve in the pathophysiology of a subtype of ASD.<br><br>METHODS: A cohort of 105 ASD children were recruited and grouped based on IFN-&#x3b3; levels derived from ex vivo stimulated &#x3b3;&#x3b4;T cells. Fecal samples were collected and analyzed with a metagenomic approach. Comparison of autistic symptoms and gut microbiota composition was made between subgroups. Enriched KEGG orthologues markers and pathogen-host interactions based on metagenome were also analyzed to reveal the differences in functional features.<br><br>RESULTS: The autistic behavioral symptoms were more severe for children in the IFN-&#x3b3;-high group, especially in the body and object use, social and self-help, and expressive language performance domains. LEfSe analysis of gut microbiota revealed an overrepresentation of Selenomonadales, Negatiyicutes, Veillonellaceae and Verrucomicrobiaceae and underrepresentation of Bacteroides xylanisolvens and Bifidobacterium longum in children with higher IFN-&#x3b3; level. Decreased metabolism function of carbohydrate, amino acid and lipid in gut microbiota were found in the IFN-&#x3b3;-high group. Additional functional profiles analyses revealed significant differences in the abundances of genes encoding carbohydrate-active enzymes between the two groups. And enriched phenotypes related to infection and gastroenteritis and underrepresentation of one gut-brain module associated with histamine degradation were also found in the IFN-&#x3b3;-High group. Results of multivariate analyses revealed relatively good separation between the two groups.<br><br>CONCLUSIONS: Levels of IFN-&#x3b3; derived from &#x3b3;&#x3b4;T cell could serve as one of the potential candidate biomarkers to subtype ASD individuals to reduce the heterogeneity associated with ASD and produce subgroups which are more likely to share a more similar phenotype and etiology. A better understanding of the associations among immune function, gut microbiota composition and metabolism abnormalities in ASD would facilitate the development of individualized biomedical treatment for this complex neurodevelopmental disorder.}, }
@article {pmid36874978, year = {2023}, author = {Fuchsman, CA and Garcia Prieto, D and Hays, MD and Cram, JA}, title = {Associations between picocyanobacterial ecotypes and cyanophage host genes across ocean basins and depth.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14924}, pmid = {36874978}, issn = {2167-8359}, abstract = {BACKGROUND: Cyanophages, viruses that infect cyanobacteria, are globally abundant in the ocean's euphotic zone and are a potentially important cause of mortality for marine picocyanobacteria. Viral host genes are thought to increase viral fitness by either increasing numbers of genes for synthesizing nucleotides for virus replication, or by mitigating direct stresses imposed by the environment. The encoding of host genes in viral genomes through horizontal gene transfer is a form of evolution that links viruses, hosts, and the environment. We previously examined depth profiles of the proportion of cyanophage containing various host genes in the Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) and at the subtropical North Atlantic (BATS). However, cyanophage host genes have not been previously examined in environmental depth profiles across the oceans.<br><br>METHODOLOGY: We examined geographical and depth distributions of picocyanobacterial ecotypes, cyanophage, and their viral-host genes across ocean basins including the North Atlantic, Mediterranean Sea, North Pacific, South Pacific, and Eastern Tropical North and South Pacific ODZs using phylogenetic metagenomic read placement. We determined the proportion of myo and podo-cyanophage containing a range of host genes by comparing to cyanophage single copy core gene terminase (terL). With this large dataset (22 stations), network analysis identified statistical links between 12 of the 14 cyanophage host genes examined here with their picocyanobacteria host ecotypes.<br><br>RESULTS: Picyanobacterial ecotypes, and the composition and proportion of cyanophage host genes, shifted dramatically and predictably with depth. For most of the cyanophage host genes examined here, we found that the composition of host ecotypes predicted the proportion of viral host genes harbored by the cyanophage community. Terminase is too conserved to illuminate the myo-cyanophage community structure. Cyanophage cobS was present in almost all myo-cyanophage and did not vary in proportion with depth. We used the composition of cobS phylotypes to track changes in myo-cyanophage composition.<br><br>CONCLUSIONS: Picocyanobacteria ecotypes shift with changes in light, temperature, and oxygen and many common cyanophage host genes shift concomitantly. However, cyanophage phosphate transporter gene pstS appeared to instead vary with ocean basin and was most abundant in low phosphate regions. Abundances of cyanophage host genes related to nutrient acquisition may diverge from host ecotype constraints as the same host can live in varying nutrient concentrations. Myo-cyanophage community in the anoxic ODZ had reduced diversity. By comparison to the oxic ocean, we can see which cyanophage host genes are especially abundant (nirA, nirC, and purS) or not abundant (myo psbA) in ODZs, highlighting both the stability of conditions in the ODZ and the importance of nitrite as an N source to ODZ endemic LLV Prochlorococcus.}, }
@article {pmid36873548, year = {2023}, author = {Tamayo-Trujillo, R and Guevara-Ramírez, P and Cadena-Ullauri, S and Paz-Cruz, E and Ruiz-Pozo, VA and Zambrano, AK}, title = {Human virome: Implications in cancer.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e14086}, pmid = {36873548}, issn = {2405-8440}, abstract = {In recent years, the human virome has gained importance, especially after the SARS-CoV-2 pandemic, due to its possible involvement in autoimmune, inflammatory diseases, and cancer. Characterization of the human virome can be carried out by shotgun next-generation sequencing (metagenomics), which allows the identification of all viral communities in an environmental sample and the discovery of new viral families not previously described. Variations in viral quantity and diversity have been associated with disease development, mainly due to their effect on gut bacterial microbiota. Phages can regulate bacterial flora through lysogeny; this is associated with increased susceptibility to infections, chronic inflammation, or cancer. The virome characterization in different human body ecological niches could help elucidate these particles' role in disease. Hence, it is important to understand the virome's influence on human health and disease. The present review highlights the significance of the human virome and how it is associated with disease, focusing on virome composition, characterization, and its association with cancer.}, }
@article {pmid36871871, year = {2023}, author = {Lei, C and Ge, H and Ding, S and Zhou, X and Yang, B and Yang, D and Wang, R and Guo, T and Yu, Y and Luo, H}, title = {Polybacterial infection in patients with stable bronchiectasis revealed by metagenomic next-generation sequencing.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jinf.2023.02.041}, pmid = {36871871}, issn = {1532-2742}, }
@article {pmid36871385, year = {2023}, author = {Liang, J and Lin, H and Singh, B and Wang, A and Yan, Z}, title = {A global perspective on compositions, risks, and ecological genesis of antibiotic resistance genes in biofilters of drinking water treatment plants.}, journal = {Water research}, volume = {233}, number = {}, pages = {119822}, doi = {10.1016/j.watres.2023.119822}, pmid = {36871385}, issn = {1879-2448}, abstract = {Antibiotic resistance genes (ARGs) in biofilters of drinking water treatment plants (DWTPs) are regarded to be a remarkable potential health risk to human. A global survey on ARGs in biofilters may help evaluate their risk features as a whole. This study aims to explore the compositions, risks, and ecological genesis of ARGs in the biofilters of DWTPs. In total, 98 metagenomes of DWTP biofilters were collected from Sequence Read Archive (SRA) of National center for Biotechnology Information (NCBI), and the main ARG types were recognized, with multidrug, bacitracin, and beta-lactam as the first three types. Source water types (surface water vs. groundwater) were found to significantly influence antibiotic resistome, overpassing biofilter media and locations. Although ARG abundances of surface water biofilters were approximately five times higher than that of groundwater biofilters, the risk pattern of ARGs was highly similar between surface water biofilters and groundwater biofilters, and up to 99.61% of the ARGs on average belong to the least risk and unassessed ranks, and only 0.23% the highest risk rank. Monobactam biosynthesis pathway and prodigiosin biosynthesis pathway, two antibiotics biosynthesis pathways, were observed to be positively correlated with several ARG types and total ARG abundance in samples of surface water and groundwater biofilters, respectively, suggesting their potential roles in ecological genesis of ARGs. Overall, the results of this study would deepen our understanding of the ARG risks in biofilters of DWTPs and shed light on their ecological genesis inside.}, }
@article {pmid36871384, year = {2023}, author = {Duan, X and Luo, J and Su, Y and Liu, C and Feng, L and Chen, Y}, title = {Proteomic profiling of robust acetoclastic methanogen in chrysene-altered anaerobic digestion: Global dissection of enzymes.}, journal = {Water research}, volume = {233}, number = {}, pages = {119817}, doi = {10.1016/j.watres.2023.119817}, pmid = {36871384}, issn = {1879-2448}, abstract = {Methanogen is a pivotal player in pollution treatment and energy recovery, and emerging pollutants (EPs) frequently occur in methanogen-applied biotechnology such as anaerobic digestion (AD). However, the direct effect and underlying mechanism of EPs on crucial methanogen involved in its application still remain unclear. The positive effect of chrysene (CH) on semi-continuous AD of sludge and the robust methanogen was dissected in this study. The methane yield in the digester with CH (100 mg/kg dry sludge) was 62.1 mL/g VS substrate, much higher than that in the control (46.1 mL/g VS substrate). Both methane production from acetoclastic methanogenesis (AM) and the AM proportion in the methanogenic pathway were improved in CH-shaped AD. Acetoclastic consortia, especially Methanosarcina and functional profiles of AM were enriched by CH in favor of the corresponding methanogenesis. Further, based on pure cultivation exposed to CH, the methanogenic performance, biomass, survivability and activity of typical Methanosarcina (M. barkeri) were boosted. Notably, iTRAQ proteomics revealed that the manufacturing (transcription and translation), expression and biocatalytic activity of acetoclastic metalloenzymes, particularly tetrahydromethanopterin S-methyltransferase and methyl-coenzyme M reductase with cobalt/nickel-cofactor (F430 and cobalamin), and acetyl-CoA decarbonylase/synthase with cobalt/nickel-active site, of M. barkeri were upregulated significantly with fold changes in the range of 1.21-3.20 due to the CH presence. This study shed light on EPs-affecting industrially crucial methanogen at the molecular biology level during AD and had implications in the technical relevance of methanogens.}, }
@article {pmid36871383, year = {2023}, author = {Lu, J and Zhang, B and Geng, R and Lian, G and Dong, H}, title = {Independent and synergistic bio-reductions of uranium (VI) driven by zerovalent iron in aquifer.}, journal = {Water research}, volume = {233}, number = {}, pages = {119778}, doi = {10.1016/j.watres.2023.119778}, pmid = {36871383}, issn = {1879-2448}, abstract = {Zerovalent iron [Fe(0)] can donate electron for bioprocess, but microbial uranium (VI) [U(VI)] reduction driven by Fe(0) is still poorly understood. In this study, Fe(0) supported U(VI) bio-reduction was steadily achieved in the 160-d continuous-flow biological column. The maximum removal efficiency and capacity of U(VI) were 100% and 46.4 ± 0.52 g/(m[3]·d) respectively, and the longevity of Fe(0) increased by 3.09 times. U(VI) was reduced to solid UO2, while Fe(0) was finally oxidized to Fe(III). Autotrophic Thiobacillus achieved U(VI) reduction coupled to Fe(0) oxidation, verified by pure culture. H2 produced from Fe(0) corrosion was consumed by autotrophic Clostridium for U(VI) reduction. The detected residual organic intermediates were biosynthesized with energy released from Fe(0) oxidation and utilized by heterotrophic Desulfomicrobium, Bacillus and Pseudomonas to reduce U(VI). Metagenomic analysis found the upregulated genes for U(VI) reduction (e.g., dsrA and dsrB) and Fe(II) oxidation (e.g., CYC1 and mtrA). These functional genes were also transcriptionally expressed. Cytochrome c and glutathione responsible for electron transfer also contributed to U(VI) reduction. This study reveals the independent and synergistic pathways for Fe(0)-dependent U(VI) bio-reduction, providing promising remediation strategy for U(VI)-polluted aquifers.}, }
@article {pmid36871189, year = {2023}, author = {Peterson, BD and Krabbenhoft, DP and McMahon, KD and Ogorek, JM and Tate, MT and Orem, WH and Poulin, BA}, title = {Environmental formation of methylmercury is controlled by synergy of inorganic mercury bioavailability and microbial mercury-methylation capacity.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16364}, pmid = {36871189}, issn = {1462-2920}, abstract = {Methylmercury (MeHg) production is controlled by the bioavailability of inorganic divalent mercury (Hg(II)i) and Hg-methylation capacity of the microbial community (conferred by the hgcAB gene cluster). However, the relative importance of these factors and their interaction in the environment remain poorly understood. Here, metagenomic sequencing and a full-factorial MeHg formation experiment were conducted across a wetland sulfate gradient with different microbial communities and pore water chemistries. From this experiment, the relative importance of each factor on MeHg formation was isolated. Hg(II)i bioavailability correlated with the dissolved organic matter composition, while the microbial Hg-methylation capacity correlated with the abundance of hgcA genes. MeHg formation responded synergistically to both factors. Notably, hgcA sequences were from diverse taxonomic groups, none of which contained genes for dissimilatory sulfate reduction. This work expands our understanding of the geochemical and microbial constraints on MeHg formation in situ and provides an experimental framework for further mechanistic studies. This article is protected by copyright. All rights reserved.}, }
@article {pmid36871069, year = {2023}, author = {Nowinski, B and Feng, X and Preston, CM and Birch, JM and Luo, H and Whitman, WB and Moran, MA}, title = {Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36871069}, issn = {1751-7370}, abstract = {Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species' divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species' pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare.}, }
@article {pmid36871005, year = {2023}, author = {Wu, TT and Sohn, M and Manning, S and Beblavy, R and Gill, S and Quataert, S and Vasani, S and Jang, H and Zeng, Y and Bruno, J and Vazquez, A and Fiscella, K and Xiao, J}, title = {Metagenomic analysis examines oral microbiome changes and interplay with immune response following prenatal total oral rehabilitation.}, journal = {Journal of translational medicine}, volume = {21}, number = {1}, pages = {172}, pmid = {36871005}, issn = {1479-5876}, abstract = {BACKGROUND: Suboptimal maternal oral health during pregnancy is potentially associated with adverse birth outcomes and increased dental caries risks in children. This study aimed to assess the oral microbiome and immune response following an innovative clinical regimen, Prenatal Total Oral Rehabilitation (PTOR), that fully restores women's oral health to a "disease-free status" before delivery.<br><br>METHODS: This prospective cohort study assessed 15 pregnant women at baseline and 3 follow-up visits (1&#xa0;week, 2&#xa0;weeks, and 2&#xa0;months) after receiving PTOR. The salivary and supragingival plaque microbiomes were analyzed using metagenomic sequencing. Multiplexed Luminex cytokine assays were performed to examine immune response following PTOR. The association between salivary immune markers and oral microbiome was further examined.<br><br>RESULTS: PTOR was associated with a reduction of periodontal pathogens in plaque, for instance, a lower relative abundance of Tannerella forsythia and Treponema denticola at 2&#xa0;weeks compared to the baseline (p&#x2009;<&#x2009;0.05). The alpha diversity of plaque microbial community was significantly reduced at the 1-week follow-up (p&#x2009;<&#x2009;0.05). Furthermore, we observed significant changes in the Actinomyces defective-associated carbohydrate degradation pathway and Streptococcus Gordonii-associated fatty acid biosynthesis pathway. Two immune markers related to adverse birth outcomes significantly differed between baseline and follow-up. ITAC, negatively correlated with preeclampsia severity, significantly increased at 1-week follow-up; MCP-1, positively correlated with gestational age, was elevated at 1-week follow-up. Association modeling between immune markers and microbiome further revealed specific oral microorganisms that are potentially correlated with the host immune response.<br><br>CONCLUSIONS: PTOR is associated with alteration of the oral microbiome and immune response among a cohort of underserved US pregnant women. Future randomized clinical trials are warranted to comprehensively assess the impact of PTOR on maternal oral flora, birth outcomes, and their offspring's oral health.}, }
@article {pmid36869541, year = {2023}, author = {Herrera-Rocha, F and Fernández-Niño, M and Cala, MP and Duitama, J and Barrios, AFG}, title = {Omics approaches to understand cocoa processing and chocolate flavor development: A review.}, journal = {Food research international (Ottawa, Ont.)}, volume = {165}, number = {}, pages = {112555}, doi = {10.1016/j.foodres.2023.112555}, pmid = {36869541}, issn = {1873-7145}, abstract = {The global market of chocolate has increased worldwide during the last decade and is expected to reach a value of USD 200 billion by 2028. Chocolate is obtained from different varieties of Theobroma cacao L, a plant domesticated more than 4000 years ago in the Amazon rainforest. However, chocolate production is a complex process requiring extensive post-harvesting, mainly involving cocoa bean fermentation, drying, and roasting. These steps have a critical impact on chocolate quality. Standardizing and better understanding cocoa processing is, therefore, a current challenge to boost the global production of high-quality cocoa worldwide. This knowledge can also help cocoa producers improve cocoa processing management and obtain a better chocolate. Several recent studies have been conducted to dissect cocoa processing via omics analysis. A vast amount of data has been produced regarding omics studies of cocoa processing performed worldwide. This review systematically analyzes the current data on cocoa omics using data mining techniques and discusses opportunities and gaps for cocoa processing standardization from this data. First, we observed a recurrent report in metagenomics studies of species of the fungi genus Candida and Pichia as well as bacteria from the genus Lactobacillus, Acetobacter, and Bacillus. Second, our analyzes of the available metabolomics data showed clear differences in the identified metabolites in cocoa and chocolate from different geographical origin, cocoa type, and processing stage. Finally, our analysis of peptidomics data revealed characteristic patterns in the gathered data including higher diversity and lower size distribution of peptides in fine-flavor cocoa. In addition, we discuss the current challenges in cocoa omics research. More research is still required to fill gaps in central matter in chocolate production as starter cultures for cocoa fermentation, flavor evolution of cocoa, and the role of peptides in the development of specific flavor notes. We also offer the most comprehensive collection of multi-omics data in cocoa processing gathered from different research articles.}, }
@article {pmid36869370, year = {2023}, author = {Gu, F and Zhu, S and Tang, Y and Liu, X and Jia, M and Malmuthuge, N and Valencak, TG and McFadden, JW and Liu, JX and Sun, HZ}, title = {Gut microbiome is linked to functions of peripheral immune cells in transition cows during excessive lipolysis.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {40}, pmid = {36869370}, issn = {2049-2618}, abstract = {BACKGROUND: Postpartum dairy cows experiencing excessive lipolysis are prone to severe immunosuppression. Despite the extensive understanding of the gut microbial regulation of host immunity and metabolism, its role during excessive lipolysis in cows is largely unknown. Herein, we investigated the potential links between the gut microbiome and postpartum immunosuppression in periparturient dairy cows with excessive lipolysis using single immune cell transcriptome, 16S amplicon sequencing, metagenomics, and targeted metabolomics.<br><br>RESULTS: The use of single-cell RNA sequencing identified 26 clusters that were annotated to 10 different immune cell types. Enrichment of functions of these clusters revealed a downregulation of functions in immune cells isolated from a cow with excessive lipolysis compared to a cow with low/normal lipolysis. The results of metagenomic sequencing and targeted metabolome analysis together revealed that secondary bile acid (SBA) biosynthesis was significantly activated in the cows with excessive lipolysis. Moreover, the relative abundance of gut Bacteroides sp. OF04&#x2009;-&#x2009;15BH, Paraprevotella clara, Paraprevotella xylaniphila, and Treponema sp. JC4 was mainly associated with SBA synthesis. The use of an integrated analysis showed that the reduction of plasma glycolithocholic acid and taurolithocholic acid could contribute to the immunosuppression of monocytes (CD14[+]MON) during excessive lipolysis by decreasing the expression of GPBAR1.<br><br>CONCLUSIONS: Our results suggest that alterations in the gut microbiota and their functions related to SBA synthesis suppressed the functions of monocytes during excessive lipolysis in transition dairy cows. Therefore, we concluded that altered microbial SBA synthesis during excessive lipolysis could lead to postpartum immunosuppression in transition cows. Video Abstract.}, }
@article {pmid36869137, year = {2023}, author = {Rifkin, RF and Vikram, S and Alcorta, J and Ramond, JB and Cowan, DA and Jakobsson, M and Schlebusch, CM and Lombard, M}, title = {Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {240}, pmid = {36869137}, issn = {2399-3642}, abstract = {The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.}, }
@article {pmid36868257, year = {2023}, author = {Rubin, DH and Mortimer, TD and Grad, YH}, title = {Neisseria gonorrhoeae diagnostic escape from a gyrA-based test for ciprofloxacin susceptibility and the effect on zoliflodacin resistance: a bacterial genetics and experimental evolution study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2666-5247(22)00356-1}, pmid = {36868257}, issn = {2666-5247}, abstract = {BACKGROUND: The aetiological bacterial agent of gonorrhoea, Neisseria gonorrhoeae, has become resistant to each of the first-line antibiotics used to treat it, including ciprofloxacin. One diagnostic approach to identify ciprofloxacin-susceptible isolates is to determine codon 91 in the gene encoding the A subunit of DNA gyrase, gyrA, where coding for the wild-type serine (gyrA[91S]) is associated with ciprofloxacin susceptibility and phenylalanine (gyrA[91F]) with resistance. The aim of this study was to investigate the possibility of diagnostic escape from gyrA susceptibility testing.<br><br>METHODS: We used bacterial genetics to introduce pairwise substitutions in GyrA positions 91 (S or F) and 95 (D, G, or N), which is a second site in GyrA associated with ciprofloxacin resistance, into five clinical isolates of N gonorrhoeae. All five isolates encoded GyrA S91F, an additional substitution in GyrA at position 95, substitutions in ParC that are known to cause an increased minimum inhibitory concentration (MIC) to ciprofloxacin, and GyrB 429D, which is associated with susceptibility to zoliflodacin (a spiropyrimidinetrione-class antibiotic in phase 3 trials for treatment of gonorrhoea). We evolved these isolates to assess for the existence of pathways to ciprofloxacin resistance (MIC &#x2265;1 &#x3bc;g/mL) and measured MICs for ciprofloxacin and zoliflodacin. In parallel, we searched metagenomic data for 11&#x2009;355 N gonorrhoeae clinical isolates with reported ciprofloxacin MICs that were publicly available from the European Nucleotide Archive for strains that would be identified as susceptible by gyrA codon 91-based assays.<br><br>FINDINGS: Three clinical isolates of N gonorrhoeae with substitutions in GyrA position 95 associated with resistance (G or N) maintained intermediate ciprofloxacin MICs (0&#xb7;125-0&#xb7;5 &#x3bc;g/mL), which has been associated with treatment failure, despite reversion of GyrA position 91 from phenylalanine to serine. From an in-silico analysis of the 11&#x2009;355 genomes from N gonorrhoeae clinical isolates, we identified 30 isolates with gyrA codon 91 encoding a serine and a ciprofloxacin resistance-associated mutation at codon 95. The reported MICs for these isolates varied from 0&#xb7;023 &#x3bc;g/mL to 0&#xb7;25 &#x3bc;g/mL, including four with intermediate ciprofloxacin MICs (associated with substantially increased risk of treatment failure). Finally, through experimental evolution, one clinical isolate of N gonorrhoeae bearing GyrA 91S acquired ciprofloxacin resistance through mutations in the gene encoding for the B subunit of DNA gyrase (gyrB) that also conferred reduced susceptibility to zoliflodacin (ie, MIC &#x2265;2 &#x3bc;g/mL).<br><br>INTERPRETATION: Diagnostic escape from gyrA codon 91 diagnostics could occur through either reversion of the gyrA allele or expansion of circulating lineages. N gonorrhoeae genomic surveillance efforts might benefit from including gyrB, given its potential for contributing to ciprofloxacin and zoliflodacin resistance, and diagnostic strategies that reduce the likelihood of escape, such as the incorporation of multiple target sites, should be investigated. Diagnostics that guide antibiotic therapy can have unintended consequences, including novel resistance determinants and antibiotic cross-resistance.<br><br>FUNDING: US National Institutes of Health National Institute of Allergy and Infectious Diseases, National Institute of General Medical Sciences, and the Smith Family Foundation.}, }
@article {pmid36868119, year = {2023}, author = {Corbera-Rubio, F and Laureni, M and Koudijs, N and Müller, S and van Alen, T and Schoonenberg, F and Lücker, S and Pabst, M and van Loosdrecht, MCM and van Halem, D}, title = {Meta-omics profiling of full-scale groundwater rapid sand filters explains stratification of iron, ammonium and manganese removals.}, journal = {Water research}, volume = {233}, number = {}, pages = {119805}, doi = {10.1016/j.watres.2023.119805}, pmid = {36868119}, issn = {1879-2448}, abstract = {Rapid sand filters (RSF) are an established and widely applied technology for groundwater treatment. Yet, the underlying interwoven biological and physical-chemical reactions controlling the sequential removal of iron, ammonia and manganese remain poorly understood. To resolve the contribution and interactions between the individual reactions, we studied two full-scale drinking water treatment plant configurations, namely (i) one dual-media (anthracite and quartz sand) filter and (ii) two single-media (quartz sand) filters in series. In situ and ex situ activity tests were combined with mineral coating characterization and metagenome-guided metaproteomics along the depth of each filter. Both plants exhibited comparable performances and process compartmentalization, with most of ammonium and manganese removal occurring only after complete iron depletion. The homogeneity of the media coating and genome-based microbial composition within each compartment highlighted the effect of backwashing, namely the complete vertical mixing of the filter media. In stark contrast to this homogeneity, the removal of the contaminants was strongly stratified within each compartment, and decreased along the filter height. This apparent and longstanding conflict was resolved by quantifying the expressed proteome at different filter heights, revealing a consistent stratification of proteins catalysing ammonia oxidation and protein-based relative abundances of nitrifying genera (up to 2 orders of magnitude difference between top and bottom samples). This implies that microorganisms adapt their protein pool to the available nutrient load at a faster rate than the backwash mixing frequency. Ultimately, these results show the unique and complementary potential of metaproteomics to understand metabolic adaptations and interactions in highly dynamic ecosystems.}, }
@article {pmid36868117, year = {2023}, author = {Hu, ZY and Lin, YP and Wang, QT and Zhang, YX and Tang, J and Hong, SD and Dai, K and Wang, S and Lu, YZ and van Loosdrecht, MCM and Wu, J and Zeng, RJ and Zhang, F}, title = {Identification and degradation of structural extracellular polymeric substances in waste activated sludge via a polygalacturonate-degrading consortium.}, journal = {Water research}, volume = {233}, number = {}, pages = {119800}, doi = {10.1016/j.watres.2023.119800}, pmid = {36868117}, issn = {1879-2448}, abstract = {By maintaining the cell integrity of waste activated sludge (WAS), structural extracellular polymeric substances (St-EPS) resist WAS anaerobic fermentation. This study investigates the occurrence of polygalacturonate in WAS St-EPS by combining chemical and metagenomic analyses that identify ∼22% of the bacteria, including Ferruginibacter and Zoogloea, that are associated with polygalacturonate production using the key enzyme EC 5.1.3.6. A highly active polygalacturonate-degrading consortium (GDC) was enriched and the potential of this GDC for degrading St-EPS and promoting methane production from WAS was investigated. The percentage of St-EPS degradation increased from 47.6% to 85.2% after inoculation with the GDC. Methane production was also increased by up to 2.3 times over a control group, with WAS destruction increasing from 11.5% to 28.4%. Zeta potential and rheological behavior confirmed the positive effect which GDC has on WAS fermentation. The major genus in the GDC was identified as Clostridium (17.1%). Extracellular pectate lyases (EC 4.2.2.2 and 4.2.2.9), excluding polygalacturonase (EC 3.2.1.15), were observed in the metagenome of the GDC and most likely play a core role in St-EPS hydrolysis. Dosing with GDC provides a good biological method for St-EPS degradation and thereby enhances the conversion of WAS to methane.}, }
@article {pmid36868045, year = {2023}, author = {Sagar, P and Aseem, A and Banjara, SK and Veleri, S}, title = {The role of food chain in antimicrobial resistance spread and One Health approach to reduce risks.}, journal = {International journal of food microbiology}, volume = {391-393}, number = {}, pages = {110148}, doi = {10.1016/j.ijfoodmicro.2023.110148}, pmid = {36868045}, issn = {1879-3460}, abstract = {The incidence of antimicrobial resistance (AMR) is rapidly spreading worldwide. It is depleting the repertoire of antibiotics in use but the pace of development of new antibiotics is stagnant for decades. Annually, millions of people are killed by AMR. This alarming situation urged both scientific and civil bodies to take steps to curb AMR as a top priority. Here we review the various sources of AMR in the environment, especially focusing on the food chain. Food chain inculcates pathogens with AMR genes and serves as a conduit for its transmission. In certain countries, the antibiotics are more used in livestock than in humans. It is also used in agriculture crops of high value products. The indiscriminate use of antibiotics in livestock and agriculture increased rapid emergence of AMR pathogens. In addition, in many countries nosocomial settings are spewing AMR pathogens, which is a serious health hazard. Both the developed and low and middle income countries (LMIC) face the phenomenon of AMR. Therefore, a comprehensive approach for monitoring all sectors of life is required to identify the emerging trend of AMR in environment. AMR genes' mode of action must be understood to develop strategies to reduce risk. The new generation sequencing technologies, metagenomics and bioinformatics capabilities can be resorted to quickly identify and characterize AMR genes. The sampling for AMR monitoring can be done from multiples nodes of the food chain as envisioned and promoted by the WHO, FAO, OIE and UNEP under the One Health approach to overcome threat of AMR pathogens.}, }
@article {pmid36867161, year = {2023}, author = {Wright, RJ and Comeau, AM and Langille, MGI}, title = {From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools.}, journal = {Microbial genomics}, volume = {9}, number = {3}, pages = {}, doi = {10.1099/mgen.0.000949}, pmid = {36867161}, issn = {2057-5858}, abstract = {In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxonomic classification methods have determined that different tools are 'best', there are two tools that have been used the most to-date: Kraken (k-mer-based classification against a user-constructed database) and MetaPhlAn (classification by alignment to clade-specific marker genes), the latest versions of which are Kraken2 and MetaPhlAn 3, respectively. We found large discrepancies in both the proportion of reads that were classified as well as the number of species that were identified when we used both Kraken2 and MetaPhlAn 3 to classify reads within metagenomes from human-associated or environmental datasets. We then investigated which of these tools would give classifications closest to the real composition of metagenomic samples using a range of simulated and mock samples and examined the combined impact of tool-parameter-database choice on the taxonomic classifications given. This revealed that there may not be a one-size-fits-all 'best' choice. While Kraken2 can achieve better overall performance, with higher precision, recall and F1 scores, as well as alpha- and beta-diversity measures closer to the known composition than MetaPhlAn 3, the computational resources required for this may be prohibitive for many researchers, and the default database and parameters should not be used. We therefore conclude that the best tool-parameter-database choice for a particular application depends on the scientific question of interest, which performance metric is most important for this question and the limit of available computational resources.}, }
@article {pmid36867151, year = {2023}, author = {Liu, D and Li, G and Hong, Z and Zhang, C and Zhu, N and Tan, Y and Gao, T}, title = {Prevalence of Multidrug-Resistant Organisms in Healthy Adults in Shenzhen, China.}, journal = {Health security}, volume = {}, number = {}, pages = {}, doi = {10.1089/hs.2022.0111}, pmid = {36867151}, issn = {2326-5108}, abstract = {Public health problems caused by the high transmission of multidrug-resistant organisms (MDROs) have attracted widespread international attention. However, studies on healthy adults in this field are scarce. In this article, we report the microbiological screening results of 180 healthy adults recruited from 1,222 participants between 2019 and 2022 in Shenzhen, China. Findings show a high MDRO carriage rate of 26.7% in those individuals who did not use any antibiotics in the past 6 months and had not been hospitalized within the past year. MDROs were mainly extended-spectrum β-lactamase-producing Escherichia coli with high resistance to cephalosporin. With the assistance of metagenomic sequencing technology, we also performed long-term observations of several participants and found that drug-resistant gene fragments were prevalent even when MDROs were not detected by drug sensitivity testing. Based on our findings, we suggest that healthcare regulators limit the medical overuse of antibiotics and enact measures to limit its nonmedical use.}, }
@article {pmid36866839, year = {2023}, author = {Li, C and Zhang, Q and Wen, Y}, title = {Intestinal tuberculosis presented as spindle cell pseudotumor in a HIV-positive case.}, journal = {Revista espanola de enfermedades digestivas}, volume = {115}, number = {}, pages = {}, doi = {10.17235/reed.2023.9533/2023}, pmid = {36866839}, issn = {1130-0108}, abstract = {MSP is a rare and atypical form of benign granulomatous inflammation characterised by tumour-like local proliferation of spindle-shaped histiocytes containing acid-fast positive mycobacteria, which should be differentiated from neoplastic lesions. A 26-year-old Chinese man complained an intermittent and mild right lower abdominal pain for 5 months in May 2022.Histopathology of biopsy samples showed Mycobacterial spindle cell pseudotumor (MSP). The test of Mycobacterium tuberculosis detected by polymerase chain reaction using intestinal tissue slice was negative. The metagenomic next-generation sequencing (BGI-Shenzhen) using formalin-fixation and paraffin-embedded intestine samples confirmed Mycobacterium tuberculosis complex (MTBC).}, }
@article {pmid36866565, year = {2023}, author = {Arzamasov, AA and Osterman, AL}, title = {Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {}, number = {}, pages = {1-23}, doi = {10.1080/10409238.2023.2182272}, pmid = {36866565}, issn = {1549-7798}, abstract = {Bifidobacteria are early colonizers of the human neonatal gut and provide multiple health benefits to the infant, including inhibiting the growth of enteropathogens and modulating the immune system. Certain Bifidobacterium species prevail in the gut of breastfed infants due to the ability of these microorganisms to selectively forage glycans present in human milk, specifically human milk oligosaccharides (HMOs) and N-linked glycans. Therefore, these carbohydrates serve as promising prebiotic dietary supplements to stimulate the growth of bifidobacteria in the guts of children suffering from impaired gut microbiota development. However, the rational formulation of milk glycan-based prebiotics requires a detailed understanding of how bifidobacteria metabolize these carbohydrates. Accumulating biochemical and genomic data suggest that HMO and N-glycan assimilation abilities vary remarkably within the Bifidobacterium genus, both at the species and strain levels. This review focuses on the delineation and genome-based comparative analysis of differences in respective biochemical pathways, transport systems, and associated transcriptional regulatory networks, providing a foundation for genomics-based projection of milk glycan utilization capabilities across a rapidly growing number of sequenced bifidobacterial genomes and metagenomic datasets. This analysis also highlights remaining knowledge gaps and suggests directions for future studies to optimize the formulation of milk-glycan-based prebiotics that target bifidobacteria.}, }
@article {pmid36865780, year = {2023}, author = {Feng, J and Zhou, L and Zhao, X and Chen, J and Li, Z and Liu, Y and Ou, L and Xie, Z and Wang, M and Yin, X and Zhang, X and Li, Y and Luo, M and Zeng, L and Yan, Q and Xie, L and Sun, L}, title = {Evaluation of environmental factors and microbial community structure in an important drinking-water reservoir across seasons.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1091818}, pmid = {36865780}, issn = {1664-302X}, abstract = {The composition of microbial communities varies in water and sediments, and changes in environmental factors have major effects on microbiomes. Here, we characterized variations in microbial communities and physicochemical factors at two sites in a large subtropical drinking water reservoir in southern China. The microbiomes of all sites, including the diversity and abundance of microbial species, were determined via metagenomics, and the relationships between microbiomes and physicochemical factors were determined via redundancy analysis. The dominant species in sediment and water samples differed; Dinobryon sp. LO226KS and Dinobryon divergens were dominant in sediment samples, whereas Candidatus Fonsibacter ubiquis and Microcystis elabens were dominant in water. The diversity was also significantly different in microbial alpha diversity between water and sediment habitats (p < 0.01). The trophic level index (TLI) was the major factor affecting the microbial community in water samples; Mycolicibacterium litorale and Mycolicibacterium phlei were significantly positively related to TLI. Furthermore, we also studied the distribution of algal toxin-encoding genes and antibiotic-resistant genes (ARGs) in the reservoir. It found that water samples contained more phycotoxin genes, with the cylindrospermopsin gene cluster most abundant. We found three genera highly related to cylindrospermopsin and explored a new cyanobacteria Aphanocapsa montana that may produce cylindrospermopsin based on the correlation through network analysis. The multidrug resistance gene was the most abundant ARG, while the relationship between ARGs and bacteria in sediment samples was more complicated than in water. The results of this study enhance our understanding of the effects of environmental factors on microbiomes. In conclusion, research on the properties, including profiles of algal toxin-encoding genes and ARGs, and microbial communities can aid water quality monitoring and conservation.}, }
@article {pmid36865186, year = {2023}, author = {Robitaille, S and Simmons, EL and Verster, AJ and McClure, EA and Royce, DB and Trus, E and Swartz, K and Schultz, D and Nadell, CD and Ross, BD}, title = {Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.02.20.529031}, pmid = {36865186}, abstract = {Understanding the relationship between the composition of the human gut microbiota and the ecological forces shaping it is of high importance as progress towards therapeutic modulation of the microbiota advances. However, given the inaccessibility of the gastrointestinal tract, our knowledge of the biogeographical and ecological relationships between physically interacting taxa has been limited to date. It has been suggested that interbacterial antagonism plays an important role in gut community dynamics, but in practice the conditions under which antagonistic behavior is favored or disfavored by selection in the gut environment are not well known. Here, using phylogenomics of bacterial isolate genomes and analysis of infant and adult fecal metagenomes, we show that the contact-dependent type VI secretion system (T6SS) is repeatedly lost from the genomes of Bacteroides fragilis in adults compare to infants. Although this result implies a significant fitness cost to the T6SS, but we could not identify in vitro conditions under which such a cost manifests. Strikingly, however, experiments in mice illustrated that the B. fragilis T6SS can be favored or disfavored in the gut environment, depending on the strains and species in the surrounding community and their susceptibility to T6SS antagonism. We use a variety of ecological modeling techniques to explore the possible local community structuring conditions that could underlie the results of our larger scale phylogenomic and mouse gut experimental approaches. The models illustrate robustly that the pattern of local community structuring in space can modulate the extent of interactions between T6SS-producing, sensitive, and resistant bacteria, which in turn control the balance of fitness costs and benefits of performing contact-dependent antagonistic behavior. Taken together, our genomic analyses, in vivo studies, and ecological theory point toward new integrative models for interrogating the evolutionary dynamics of type VI secretion and other predominant modes of antagonistic interaction in diverse microbiomes.}, }
@article {pmid36864882, year = {2023}, author = {Wang, M and Yan, LY and Qiao, CY and Zheng, CC and Niu, CG and Huang, ZW and Pan, YH}, title = {Ecological shifts of salivary microbiota associated with metabolic-associated fatty liver disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1131255}, pmid = {36864882}, issn = {2235-2988}, abstract = {INTRODUCTION: Metabolic-associated fatty liver disease (MAFLD) is the most common chronic liver disease related to metabolic syndrome. However, ecological shifts in the saliva microbiome in patients with MAFLD remain unknown. This study aimed to investigate the changes to the salivary microbial community in patients with MAFLD and explore the potential function of microbiota.<br><br>METHODS: Salivary microbiomes from ten MAFLD patients and ten healthy participants were analyzed by 16S rRNA amplicon sequencing and bioinformatics analysis. Body composition, plasma enzymes, hormones, and blood lipid profiles were assessed with physical examinations and laboratory tests.<br><br>RESULTS: The salivary microbiome of MAFLD patients was characterized by increased &#x3b1;-diversity and distinct &#x3b2;-diversity clustering compared with control subjects. Linear discriminant analysis effect size analysis showed a total of 44 taxa significantly differed between the two groups. Genera Neisseria, Filifactor, and Capnocytophaga were identified as differentially enriched genera for comparison of the two groups. Co-occurrence networks suggested that the salivary microbiota from MAFLD patients exhibited more intricate and robust interrelationships. The diagnostic model based on the salivary microbiome achieved a good diagnostic power with an area under the curve of 0.82(95% CI: 0.61-1). Redundancy analysis and spearman correlation analysis revealed that clinical variables related to insulin resistance and obesity were strongly associated with the microbial community. Metagenomic predictions based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States revealed that pathways related to metabolism were more prevalent in the two groups.<br><br>CONCLUSIONS: Patients with MAFLD manifested ecological shifts in the salivary microbiome, and the saliva microbiome-based diagnostic model provides a promising approach for auxiliary MAFLD diagnosis.}, }
@article {pmid36864573, year = {2023}, author = {Cheung, MK and Ng, RWY and Lai, CKC and Zhu, C and Au, ETK and Yau, JWK and Li, C and Wong, HC and Wong, BCK and Kwok, KO and Chen, Z and Chan, PKS and Lui, GCY and Ip, M}, title = {Alterations in faecal microbiome and resistome in Chinese international travellers: a metagenomic analysis.}, journal = {Journal of travel medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/jtm/taad027}, pmid = {36864573}, issn = {1708-8305}, abstract = {BACKGROUND: International travel increases the risk of acquisition of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). Previous studies have characterized the changes in the gut microbiome and resistome of Western travellers; however, information on non-Western populations and the effects of travel-related risk factors on the gut microbiome and resistome remain limited.<br><br>METHODS: We conducted a prospective observational study on a cohort of 90 healthy Chinese adult residents of Hong Kong. We characterized the microbiome and resistome in stools collected from the subjects before and after travelling to diverse international locations using shotgun metagenomic sequencing and examined their associations with travel-related variables.<br><br>RESULTS: Our results showed that travel neither significantly changed the taxonomic composition of the faecal microbiota nor altered the alpha (Shannon) or beta diversity of the faecal microbiome or resistome. However, travel significantly increased the number of ARGs. Ten ARGs, including aadA, TEM, mgrB, mphA, qnrS9, and tetR, were significantly enriched in relative abundance after travel, eight of which were detected in metagenomic bins belonging to Escherichia/Shigella flexneri in the post-trip samples. Thirty ARGs significantly increased in prevalence after travel, with the largest changes observed in tetD and a few qnrS variants (qnrS9, qnrS and qnrS8). We found that travel to low- or middle-income countries, or Africa or Southeast Asia increased the number of ARG subtypes, whereas travel to low- or middle-income countries and the use of alcohol-based hand sanitizer (ABHS) or doxycycline as antimalarial prophylaxis during travel resulted in increased changes in the beta diversity of the faecal resistome.<br><br>CONCLUSIONS: Our study highlights travel to low- or middle-income countries, Africa or Southeast Asia, a long travel duration, or the use of ABHS or doxycycline as antimalarial prophylaxis as important risk factors for the acquisition/enrichment of ARGs during international travel.}, }
@article {pmid36864529, year = {2023}, author = {Zhang, C and Fang, YX and Yin, X and Lai, H and Kuang, Z and Zhang, T and Xu, XP and Wegener, G and Wang, JH and Dong, X}, title = {The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {37}, pmid = {36864529}, issn = {2049-2618}, abstract = {BACKGROUND: Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization.<br><br>RESULTS: Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons.<br><br>CONCLUSIONS: These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes. Video Abstract.}, }
@article {pmid36864482, year = {2023}, author = {Lou, YC and Hoff, J and Olm, MR and West-Roberts, J and Diamond, S and Firek, BA and Morowitz, MJ and Banfield, JF}, title = {Using strain-resolved analysis to identify contamination in metagenomics data.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {36}, pmid = {36864482}, issn = {2049-2618}, support = {RAI092531A/NH/NIH HHS/United States ; RAI092531A/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Metagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study itself remains underreported.<br><br>RESULTS: Here, we applied high-resolution strain-resolved analyses to identify contamination in two large-scale clinical metagenomics datasets. By mapping strain sharing to DNA extraction plates, we identified well-to-well contamination in both negative controls and biological samples in one dataset. Such contamination is more likely to occur among samples that are on the same or adjacent columns or rows of the extraction plate than samples that are far apart. Our strain-resolved workflow also reveals the presence of externally derived contamination, primarily in the other dataset. Overall, in both datasets, contamination is more significant in samples with lower biomass.<br><br>CONCLUSION: Our work demonstrates that genome-resolved strain tracking, with its essentially genome-wide nucleotide-level resolution, can be used to detect contamination in sequencing-based microbiome studies. Our results underscore the value of strain-specific methods to detect contamination and the critical importance of looking for contamination beyond negative and positive controls. Video Abstract.}, }
@article {pmid36864192, year = {2023}, author = {Katoh, T and Yamada, C and Wallace, MD and Yoshida, A and Gotoh, A and Arai, M and Maeshibu, T and Kashima, T and Hagenbeek, A and Ojima, MN and Takada, H and Sakanaka, M and Shimizu, H and Nishiyama, K and Ashida, H and Hirose, J and Suarez-Diez, M and Nishiyama, M and Kimura, I and Stubbs, KA and Fushinobu, S and Katayama, T}, title = {A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.}, journal = {Nature chemical biology}, volume = {}, number = {}, pages = {}, pmid = {36864192}, issn = {1552-4469}, abstract = {Mucinolytic bacteria modulate host-microbiota symbiosis and dysbiosis through their ability to degrade mucin O-glycans. However, how and to what extent bacterial enzymes are involved in the breakdown process remains poorly understood. Here we focus on a glycoside hydrolase family 20 sulfoglycosidase (BbhII) from Bifidobacterium bifidum, which releases N-acetylglucosamine-6-sulfate from sulfated mucins. Glycomic analysis showed that, in addition to sulfatases, sulfoglycosidases are involved in mucin O-glycan breakdown in vivo and that the released N-acetylglucosamine-6-sulfate potentially affects gut microbial metabolism, both of which were also supported by a metagenomic data mining analysis. Enzymatic and structural analysis of BbhII reveals the architecture underlying its specificity and the presence of a GlcNAc-6S-specific carbohydrate-binding module (CBM) 32 with a distinct sugar recognition mode that B. bifidum takes advantage of to degrade mucin O-glycans. Comparative analysis of the genomes of prominent mucinolytic bacteria also highlights a CBM-dependent O-glycan breakdown strategy used by B. bifidum.}, }
@article {pmid36864114, year = {2023}, author = {Wang, X and Wang, S and Yang, Y and Tian, H and Jetten, MSM and Song, C and Zhu, G}, title = {Hot moment of N2O emissions in seasonally frozen peatlands.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36864114}, issn = {1751-7370}, abstract = {Since the start of the Anthropocene, northern seasonally frozen peatlands have been warming at a rate of 0.6 °C per decade, twice that of the Earth's average rate, thereby triggering increased nitrogen mineralization with subsequent potentially large losses of nitrous oxide (N2O) to the atmosphere. Here we provide evidence that seasonally frozen peatlands are important N2O emission sources in the Northern Hemisphere and the thawing periods are the hot moment of annual N2O emissions. The flux during the hot moment of thawing in spring was 1.20 ± 0.82 mg N2O m[-2] d[-1], significantly higher than that during the other periods (freezing, -0.12 ± 0.02 mg N2O m[-2] d[-1]; frozen, 0.04 ± 0.04 mg N2O m[-2] d[-1]; thawed, 0.09 ± 0.01 mg N2O m[-2] d[-1]) or observed for other ecosystems at the same latitude in previous studies. The observed emission flux is even higher than those of tropical forests, the World's largest natural terrestrial N2O source. Furthermore, based on soil incubation with [15]N and [18]O isotope tracing and differential inhibitors, heterotrophic bacterial and fungal denitrification was revealed as the main source of N2O in peatland profiles (0-200 cm). Metagenomic, metatranscriptomic, and qPCR assays further revealed that seasonally frozen peatlands have high N2O emission potential, but thawing significantly stimulates expression of genes encoding N2O-producing protein complexes (hydroxylamine dehydrogenase (hao) and nitric oxide reductase (nor)), resulting in high N2O emissions during spring. This hot moment converts seasonally frozen peatlands into an important N2O emission source when it is otherwise a sink. Extrapolation of our data to all northern peatland areas reveals that the hot moment emissions could amount to approximately 0.17 Tg of N2O yr[-1]. However, these N2O emissions are still not routinely included in Earth system models and global IPCC assessments.}, }
@article {pmid36864029, year = {2023}, author = {Lee, K and Raguideau, S and Sirén, K and Asnicar, F and Cumbo, F and Hildebrand, F and Segata, N and Cha, CJ and Quince, C}, title = {Population-level impacts of antibiotic usage on the human gut microbiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1191}, pmid = {36864029}, issn = {2041-1723}, abstract = {The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.}, }
@article {pmid36863655, year = {2023}, author = {Wang, G and Qiu, G and Wei, J and Guo, Z and Wang, W and Liu, X and Song, Y}, title = {Activated carbon enhanced traditional activated sludge process for chemical explosion accident wastewater treatment.}, journal = {Environmental research}, volume = {}, number = {}, pages = {115595}, doi = {10.1016/j.envres.2023.115595}, pmid = {36863655}, issn = {1096-0953}, abstract = {With the development of industries, explosion accidents occur frequently during production, transportation, usage and storage of hazard chemicals. It remained challenging to efficiently treat the resultant wastewater. As an enhancement of traditional process, the activated carbon-activated sludge (AC-AS) process has a promising potential in treating wastewater with high concentrations of toxic compounds, chemical oxygen demand (COD) and ammonia nitrogen (NH4[+]-N), etc. In this paper, activated carbon (AC), activated sludge (AS) and AC-AS were used to treat the wastewater produced from an explosion accident in the Xiangshui Chemical Industrial Park. The removal efficiency was assessed by the removal performances of COD, dissolved organic carbon (DOC), NH4[+]-N, aniline and nitrobenzene. Increased removal efficiency and shortened treatment time were achieved in the AC-AS system. To achieve the same COD, DOC and aniline removal (90%), the AC-AS system saved 30, 38 and 58 h compared with the AS system, respectively. The enhancement mechanism of AC on the AS was explored by metagenomic analysis and three-dimensional excitation-emission-matrix spectra (3DEEMs). More organics, especially aromatic substances were removed in the AC-AS system. These results showed that the addition of AC promoted the microbial activity in pollutant degradation. Bacteria, such as Pyrinomonas, Acidobacteria and Nitrospira and genes, such as hao, pmoA-amoA, pmoB-amoB and pmoC-amoC, were found in the AC-AS reactor, which might have played important roles in the degradation of pollutants. To sum up, AC might have enhanced the growth of aerobic bacteria which further improved the removal efficiency via the combined effects of adsorption and biodegradation. The successful treatment of Xiangshui accident wastewater using the AC-AS demonstrated the potential universal characteristics of the process for the treatment of wastewater with high concentration of organic matter and toxicity. This study is expected to provide reference and guidance for the treatment of similar accident wastewaters.}, }
@article {pmid36863103, year = {2023}, author = {Huang, J and Dai, X and Chen, X and Ali, I and Chen, H and Gou, J and Zhuo, C and Huang, M and Zhu, B and Tang, Y and Liu, J and Xu, Y and Tang, F and Xue, J}, title = {Combined forage grass-microbial for remediation of strontium-contaminated soil.}, journal = {Journal of hazardous materials}, volume = {450}, number = {}, pages = {131013}, doi = {10.1016/j.jhazmat.2023.131013}, pmid = {36863103}, issn = {1873-3336}, abstract = {Enrichment plants were screened from six forage grasses in this study to establish a complete combined forage grass-microbial remediation system of strontium-contaminated soil, and microbial groups were added to the screened dominant forage grasses. The occurrence states of strontium in forage grasses were explored by the BCR sequential extraction method. The results showed that the annual removal rate of Sudan grass (Sorghum sudanense (Piper) Stapf.) reached 23.05% in soil with a strontium concentration of 500 mg·kg[-1]. Three dominant microbial groups: E, G and H, have shown good facilitation effects in co-remediation with Sudan grass and Gaodan grass (Sorghum bicolor × sudanense), respectively. When compared to the control, the strontium accumulation of forage grasses in kg of soil with microbial groups was increased by 0.5-4 fold. The optimal forage grass-microbial combination can theoretically repair contaminated soil in three years. The microbial group E was found to promote the transfer of the exchangeable state and the reducible state of strontium to the overground part of the forage grass. Metagenomic sequencing results showed that the addition of microbial groups increased Bacillus spp. in rhizosphere soil, enhanced the disease resistance and tolerance of forage grasses, and improved the remediation ability of forage grass-microbial combinations.}, }
@article {pmid36863003, year = {2023}, author = {Xu, G and Hou, B and Xue, C and Xu, Q and Qu, L and Hao, X and Liu, Y and Wang, D and Li, Z and Jin, X}, title = {Acute Retinal Necrosis Associated with Pseudorabies Virus Infection: A Case Report and Literature Review.}, journal = {Ocular immunology and inflammation}, volume = {}, number = {}, pages = {1-8}, doi = {10.1080/09273948.2023.2181188}, pmid = {36863003}, issn = {1744-5078}, abstract = {PURPOSE: To analyze a case of acute retinal necrosis (ARN) associated with pseudorabies virus (PRV) infection and discusses the clinical characteristics of PRV-induced ARN (PRV-ARN).<br><br>METHODS: Case report and literature review of ocular features in PRV-ARN.<br><br>RESULTS: A 52-year-old female diagnosed with encephalitis presented with bilateral vision loss, mild anterior uveitis, vitreous opacity, occlusive retinal vasculitis, and retinal detachment in her left eye. The result of metagenomic next-generation sequencing (mNGS) indicated that both cerebrospinal fluids and vitreous fluid tested positive for PRV.<br><br>CONCLUSION: PRV, a zoonosis, can infect both humans and mammals. Patients affected with PRV may experience severe encephalitis and oculopathy, and the infection has been associated with high mortality and disability. ARN is the most common ocular disease, which develops rapidly following encephalitis and is characterized by five figures: bilateral onset, rapid progression, severe visual impairment, poor response to systemic antiviral drugs, and an unfavorable prognosis.}, }
@article {pmid36862944, year = {2023}, author = {Amarelle, V and Roldán, DM and Fabiano, E and Guazzaroni, ME}, title = {Synthetic Biology Toolbox for Antarctic Pseudomonas sp. Strains: Toward a Psychrophilic Nonmodel Chassis for Function-Driven Metagenomics.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.2c00543}, pmid = {36862944}, issn = {2161-5063}, abstract = {One major limitation of function-driven metagenomics is the ability of the host to express the metagenomic DNA correctly. Differences in the transcriptional, translational, and post-translational machinery between the organism to which the DNA belongs and the host strain are all factors that influence the success of a functional screening. For this reason, the use of alternative hosts is an appropriate approach to favor the identification of enzymatic activities in function-driven metagenomics. To be implemented, appropriate tools should be designed to build the metagenomic libraries in those hosts. Moreover, discovery of new chassis and characterization of synthetic biology toolbox in nonmodel bacteria is an active field of research to expand the potential of these organisms in processes of industrial interest. Here, we assessed the suitability of two Antarctic psychrotolerant Pseudomonas strains as putative alternative hosts for function-driven metagenomics using pSEVA modular vectors as scaffold. We determined a set of synthetic biology tools suitable for these hosts and, as a proof of concept, we demonstrated their fitness for heterologous protein expression. These hosts represent a step forward for the prospection and identification of psychrophilic enzymes of biotechnological interest.}, }
@article {pmid36862673, year = {2023}, author = {Lappa, D and Meijnikman, AS and Krautkramer, KA and Olsson, LM and Aydin, &#xd6; and Van Rijswijk, AS and Acherman, YIZ and De Brauw, ML and Tremaroli, V and Olofsson, LE and Lundqvist, A and Hjorth, SA and Ji, B and Gerdes, VEA and Groen, AK and Schwartz, TW and Nieuwdorp, M and Bäckhed, F and Nielsen, J}, title = {Self-organized metabotyping of obese individuals identifies clusters responding differently to bariatric surgery.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0279335}, doi = {10.1371/journal.pone.0279335}, pmid = {36862673}, issn = {1932-6203}, abstract = {Weight loss through bariatric surgery is efficient for treatment or prevention of obesity related diseases such as type 2 diabetes and cardiovascular disease. Long term weight loss response does, however, vary among patients undergoing surgery. Thus, it is difficult to identify predictive markers while most obese individuals have one or more comorbidities. To overcome such challenges, an in-depth multiple omics analyses including fasting peripheral plasma metabolome, fecal metagenome as well as liver, jejunum, and adipose tissue transcriptome were performed for 106 individuals undergoing bariatric surgery. Machine leaning was applied to explore the metabolic differences in individuals and evaluate if metabolism-based patients' stratification is related to their weight loss responses to bariatric surgery. Using Self-Organizing Maps (SOMs) to analyze the plasma metabolome, we identified five distinct metabotypes, which were differentially enriched for KEGG pathways related to immune functions, fatty acid metabolism, protein-signaling, and obesity pathogenesis. The gut metagenome of the most heavily medicated metabotypes, treated simultaneously for multiple cardiometabolic comorbidities, was significantly enriched in Prevotella and Lactobacillus species. This unbiased stratification into SOM-defined metabotypes identified signatures for each metabolic phenotype and we found that the different metabotypes respond differently to bariatric surgery in terms of weight loss after 12 months. An integrative framework that utilizes SOMs and omics integration was developed for stratifying a heterogeneous bariatric surgery cohort. The multiple omics datasets described in this study reveal that the metabotypes are characterized by a concrete metabolic status and different responses in weight loss and adipose tissue reduction over time. Our study thus opens a path to enable patient stratification and hereby allow for improved clinical treatments.}, }
@article {pmid36862079, year = {2023}, author = {Pino, V and Fajardo, M and McBratney, A and Minasny, B and Wilson, N and Baldock, C}, title = {Australian soil microbiome: a first sightseeing regional prediction driven by cycles of soil temperature and pedogenic variations.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16911}, pmid = {36862079}, issn = {1365-294X}, abstract = {To what extent does soil multifunctionality depend on soil microbiome diversity? So far, a decline in soil capacity (e.g., as a provider of food and energy) and microbial diversity might be closely related. In that case, these relationships need quantification on which analyses of community dissimilarities (β-diversity) advantage for conservation purposes. However, soil-microbes' interactions within environmental gradients are endless, and the main ecological drivers may not be consistent across studies complicating global assessments. Then, exploratory spatial modelling and mapping by simplifying complex multivariate interactions refine our understanding on ecological drivers as expand gradients to where more observations are needed. This study represents the first spatial projection of the soil microbiome β-diversity in New South Wales (800,642 km2), Australia. We used metabarcoding soil data (16S rRNA and ITS genes) as exact sequence variants (ASVs) and UMAP (Uniform Manifold Approximation and Projection) as the distance metric. β-diversity maps (1,000 m resolution) - concordance correlations between 0.91 to 0.96 and 0.91 to 0.95 for bacteria and fungi, respectively - showed soil biomes' dissimilarities driven primarily by soil chemistry - pH and Effective Cation Exchange Capacity (ECEC) - and cycles of soil temperature - land surface temperature (LST-phase and LST-amplitude). Regionally, the spatial microbial patterns parallel the distribution of soil classes (e.g., Vertosols) beyond spatial distances and rainfall, for example. Soil classes can be valuable discriminants for monitoring approaches, e.g., pedogenons and pedophenons. Ultimately, cultivated soils exhibited lower richness due to declines in rare microbes which might compromise soil functions over time.}, }
@article {pmid36861850, year = {2023}, author = {Ordinola-Zapata, R and Costalonga, M and Dietz, M and Lima, BP and Staley, C}, title = {The Root Canal Microbiome Diversity and Function. A Whole- Metagenome Shotgun analysis.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.13911}, pmid = {36861850}, issn = {1365-2591}, abstract = {AIM: Evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome shotgun sequencing.<br><br>METHODOLOGY: Twenty-two samples from patients with primary root canal infections, and eighteen samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analyzed with whole metagenome shotgun sequencing at a depth of 20M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray-Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes.<br><br>RESULTS: Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity P =&#x2009;0.001). Community composition was significantly different in primary versus secondary infection (R&#xa0;=&#xa0;0.11, P =&#x2009;0.005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signaling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, hemolysins, thiol- activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase.<br><br>CONCLUSIONS: Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar.}, }
@article {pmid36861357, year = {2023}, author = {Soto, MA and Desai, D and Bannon, C and LaRoche, J and Bertrand, EM}, title = {Cobalamin producers and prokaryotic consumers in the Northwest Atlantic.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16363}, pmid = {36861357}, issn = {1462-2920}, abstract = {Cobalamin availability can influence primary productivity and ecological interactions in marine microbial communities. The characterization of cobalamin sources and sinks is a first step in investigating cobalamin dynamics and its impact on productivity. Here we identify potential cobalamin sources and sinks on the Scotian Shelf and Slope in the Northwest Atlantic Ocean. Functional and taxonomic annotation of bulk metagenomic reads, combined with analysis of genome bins, were used to identify potential cobalamin sources and sinks. Cobalamin synthesis potential was mainly attributed to Rhodobacteraceae, Thaumarchaeota, and cyanobacteria (Synechococcus and Prochlorococcus). Cobalamin remodeling potential was mainly attributed to Alteromonadales, Pseudomonadales, Rhizobiales, Oceanospirilalles, Rhodobacteraceae, and Verrucomicrobia, while potential cobalamin consumers include Flavobacteriaceae, Actinobacteria, Porticoccaceae, Methylophiliaceae, and Thermoplasmatota. These complementary approaches identified taxa with the potential to be involved in cobalamin cycling on the Scotian Shelf and revealed genomic information required for further characterization. The Cob operon of Rhodobacterales bacterium HTCC2255, a strain with known importance in cobalamin cycling, was similar to a major cobalamin producer bin, suggesting that a related strain may represent a critical cobalamin source in this region. These results enable future inquiries that will enhance our understanding of how cobalamin shapes microbial interdependencies and productivity in this region. This article is protected by copyright. All rights reserved.}, }
@article {pmid36860485, year = {2023}, author = {Li, Y and Yan, Y and Fu, H and Jin, S and He, S and Wang, Z and Dong, G and Li, B and Guo, S}, title = {Does diet or macronutrients intake drive the structure and function of gut microbiota?.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1126189}, pmid = {36860485}, issn = {1664-302X}, abstract = {Shift of ingestive behavior is an important strategy for animals to adapt to change of the environment. We knew that shifts in animal dietary habits lead to changes in the structure of the gut microbiota, but we are not sure about if changes in the composition and function of the gut microbiota respond to changes in the nutrient intake or food items. To investigate how animal feeding strategies affect nutrient intakes and thus alter the composition and digestion function of gut microbiota, we selected a group of wild primate group for the study. We quantified their diet and macronutrients intake in four seasons of a year, and instant fecal samples were analyzed by high-throughput sequencing of 16S rRNA and metagenomics. These results demonstrated that the main reason that causes seasonal shifts of gut microbiota is the macronutrient variation induced by seasonal dietary differences. Gut microbes can help to compensate for insufficient macronutrients intake of the host through microbial metabolic functions. This study contributes to a deeper understanding of the causes of seasonal variation in host-microbial variation in wild primates.}, }
@article {pmid36860407, year = {2023}, author = {Nguyen, DH and Chu, NH and Bettarel, Y and Auguet, JC and Bouvier, T and Chu, HH and Bui, VN}, title = {Metagenomic data of bacterial communities associated with Acropora species from Phu Quoc Islands, Vietnam.}, journal = {Data in brief}, volume = {47}, number = {}, pages = {108977}, pmid = {36860407}, issn = {2352-3409}, abstract = {Acropora is one of the most common coral genera found in Phu Quoc Islands, Vietnam. However, the presence of marine snails, such as the coralllivorous gastropod Drupella rugosa, was a potential threat to the survival of many scleractinian species, leading to changes in the health status and bacterial diversity of coral reefs in Phu Quoc Islands. Here, we describe the composition of bacterial communities associated with two species of Acropora (Acropora formosa and Acropora millepora) using the Illumina sequencing technology. This dataset includes 5 coral samples of each status (grazed or healthy), which were collected in Phu Quoc Islands (9°55'20.6″N 104°01'16.4″E) in May 2020. A total of 19 phyla, 34 classes, 98 orders, 216 families and 364 bacterial genera were detected from 10 coral samples. Overall, Proteobacteria and Firmicutes were the two most common bacterial phyla in all samples. Significant differences in the relative abundances of the genera Fusibacter, Halarcobacter, Malaciobacter, and Thalassotalea between grazed and healthy status were observed. However, there was no differences in alpha diversity indices between the two status. Furthermore, the dataset analysis also indicated that Vibrio and Fusibacter were core genera in the grazed samples, whereas Pseudomonas was the core genus in the healthy samples.}, }
@article {pmid36860056, year = {2023}, author = {Chen, X and Ke, Y and Zhu, Y and Xu, M and Chen, C and Xie, S}, title = {Enrichment of tetracycline-degrading bacterial consortia: Microbial community succession and degradation characteristics and mechanism.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130984}, doi = {10.1016/j.jhazmat.2023.130984}, pmid = {36860056}, issn = {1873-3336}, abstract = {Tetracycline (TC) is an antibiotic that is recently found as an emerging pollutant with low biodegradability. Biodegradation shows great potential for TC dissipation. In this study, two TC-degrading microbial consortia (named SL and SI) were respectively enriched from activated sludge and soil. Bacterial diversity decreased in these finally enriched consortia compared with the original microbiota. Moreover, most ARGs quantified during the acclimation process became less abundant in the finally enriched microbial consortia. Microbial compositions of the two consortia as revealed by 16 S rRNA sequencing were similar to some extent, and the dominant genera Pseudomonas, Sphingobacterium, and Achromobacter were identified as the potential TC degraders. In addition, consortia SL and SI were capable of biodegrading TC (initial 50 mg/L) by 82.92% and 86.83% within 7 days, respectively. They could retain high degradation capabilities under a wide pH range (4-10) and at moderate/high temperatures (25-40 °C). Peptone with concentrations of 4-10 g/L could serve as a desirable primary growth substrate for consortia to remove TC through co-metabolism. A total of 16 possible intermediates including a novel biodegradation product TP245 were detected during TC degradation. Peroxidase genes, tetX-like genes and the enriched genes related to aromatic compound degradation as revealed by metagenomic sequencing were likely responsible for TC biodegradation.}, }
@article {pmid36860032, year = {2023}, author = {Ge, L and Song, L and Wang, L and Li, Y and Sun, Y and Wang, C and Chen, J and Wu, G and Pan, A and Wu, Y and Quan, Z and Li, P}, title = {Evaluating response mechanisms of soil microbiomes and metabolomes to Bt toxin additions.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130904}, doi = {10.1016/j.jhazmat.2023.130904}, pmid = {36860032}, issn = {1873-3336}, abstract = {The accumulation and persistence of Bt toxins in soils from Bt plants and Bt biopesticides may result in environmental hazards such as adverse impacts on soil microorganisms. However, the dynamic relationships among exogenous Bt toxins, soil characteristics, and soil microorganisms are not well understood. Cry1Ab is one of the most commonly used Bt toxins and was added to soils in this study to evaluate subsequent changes in soil physiochemical properties, microbial taxa, microbial functional genes, and metabolites profiles via 16S rRNA gene pyrosequencing, high-throughput qPCR, metagenomic shotgun sequencing, and untargeted metabolomics. Higher additions of Bt toxins led to higher concentrations of soil organic matter (SOM), ammonium (NH[+]4-N), and nitrite (NO2[-]-N) compared against controls without addition after 100 days of soil incubation. High-throughput qPCR analysis and shotgun metagenomic sequencing analysis revealed that the 500 ng/g Bt toxin addition significantly affected profiles of soil microbial functional genes involved in soil carbon (C), nitrogen (N), and phosphorus (P) cycling after 100 days of incubation. Furthermore, combined metagenomic and metabolomic analyses indicated that the 500 ng/g Bt toxin addition significantly altered low molecular weight metabolite profiles of soils. Importantly, some of these altered metabolites are involved in soil nutrient cycling, and robust associations were identified among differentially abundant metabolites and microorganisms due to Bt toxin addition treatments. Taken together, these results suggest that higher levels of Bt toxin addition can alter soil nutrients, probably by affecting the activities of Bt toxin-degrading microorganisms. These dynamics would then activate other microorganisms involved in nutrient cycling, finally leading to broad changes in metabolite profiles. Notably, the addition of Bt toxins did not cause the accumulation of potential microbial pathogens in soils, nor did it adversely affect the diversity and stability of microbial communities. This study provides new insights into the putative mechanistic associations among Bt toxins, soil characteristics, and microorganisms, providing new understanding into the ecological impacts of Bt toxins on soil ecosystems.}, }
@article {pmid36859706, year = {2023}, author = {Pinheiro, Y and Faria da Mota, F and Peixoto, RS and van Elsas, JD and Lins, U and Mazza Rodrigues, JL and Rosado, AS}, title = {A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {230}, pmid = {36859706}, issn = {2399-3642}, abstract = {A thermophilic, chemolithoautotrophic, and aerobic microbial consortium (termed carbonitroflex) growing in a nutrient-poor medium and an atmosphere containing N2, O2, CO2, and CO is investigated as a model to expand our understanding of extreme biological systems. Here we show that the consortium is dominated by Carbonactinospora thermoautotrophica (strain StC), followed by Sphaerobacter thermophilus, Chelatococcus spp., and Geobacillus spp. Metagenomic analysis of the consortium reveals a mutual relationship among bacteria, with C. thermoautotrophica StC exhibiting carboxydotrophy and carbon-dioxide storage capacity. C. thermoautotrophica StC, Chelatococcus spp., and S. thermophilus harbor genes encoding CO dehydrogenase and formate oxidase. No pure cultures were obtained under the original growth conditions, indicating that a tightly regulated interactive metabolism might be required for group survival and growth in this extreme oligotrophic system. The breadwinner hypothesis is proposed to explain the metabolic flux model and highlight the vital role of C. thermoautotrophica StC (the sole keystone species and primary carbon producer) in the survival of all consortium members. Our data may contribute to the investigation of complex interactions in extreme environments, exemplifying the interconnections and dependency within microbial communities.}, }
@article {pmid36859551, year = {2023}, author = {Chazan, A and Das, I and Fujiwara, T and Murakoshi, S and Rozenberg, A and Molina-Márquez, A and Sano, FK and Tanaka, T and Gómez-Villegas, P and Larom, S and Pushkarev, A and Malakar, P and Hasegawa, M and Tsukamoto, Y and Ishizuka, T and Konno, M and Nagata, T and Mizuno, Y and Katayama, K and Abe-Yoshizumi, R and Ruhman, S and Inoue, K and Kandori, H and León, R and Shihoya, W and Yoshizawa, S and Sheves, M and Nureki, O and Béjà, O}, title = {Phototrophy by antenna-containing rhodopsin pumps in aquatic environments.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {36859551}, issn = {1476-4687}, abstract = {Energy transfer from light-harvesting ketocarotenoids to the light-driven proton pump xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium[1] and a terrestrial cyanobacterium[2]. Attempts to find carotenoids that bind and transfer energy to abundant rhodopsin proton pumps[3] from marine photoheterotrophs have thus far failed[4-6]. Here we detected light energy transfer from the widespread hydroxylated carotenoids zeaxanthin and lutein to the retinal moiety of xanthorhodopsins and proteorhodopsins using functional metagenomics combined with chromophore extraction from the environment. The light-harvesting carotenoids transfer up to 42% of the harvested energy in the violet- or blue-light range to the green-light absorbing retinal chromophore. Our data suggest that these antennas may have a substantial effect on rhodopsin phototrophy in the world's lakes, seas and oceans. However, the functional implications of our findings are yet to be discovered.}, }
@article {pmid36857890, year = {2023}, author = {Liu, Z and Wan, X and Zhang, C and Cai, M and Pan, Y and Li, M}, title = {Deep sequencing reveals comprehensive insight into the prevalence, mobility, and hosts of antibiotic resistance genes in mangrove ecosystems.}, journal = {Journal of environmental management}, volume = {335}, number = {}, pages = {117580}, doi = {10.1016/j.jenvman.2023.117580}, pmid = {36857890}, issn = {1095-8630}, abstract = {Mangrove receives aquaculture wastewater and urban sewage, and thus is a potential reservoir for antibiotic resistance genes (ARGs). However, there is a dearth of a comprehensive profile of ARGs in mangrove ecosystems. We used metagenomic techniques to uncover the occurrence, host range, and potential mobility of ARGs in six mangrove ecosystems in southeastern China. Based on deep sequencing data, a total of 348 ARG subtypes were identified. The abundant ARGs were associated with acriflavine, bacitracin, beta-lactam, fluoroquinolone, macrolide-lincosamide-streptogramin, and polymyxin. Resistance genes tetR, aac(6')-Iae, aac(3)-IXa, vanRA, vanRG, and aac(3)-Ig were proposed as ARG indicators in mangrove ecosystems that can be used to evaluate the abundance of 100 other co-occurring ARGs quantitatively. Remarkably, 250 of 348 identified ARG subtypes were annotated as mobile genetic elements-associated ARGs, indicating a high potential risk of propagation of ARGs in mangrove ecosystems. By surveying the distribution of ARGs in 6281 draft genomes, more than 42 bacterial phyla were identified as the putative hosts of the ARGs. Among them, 21.97% were potentially multidrug-resistant hosts, including human and animal opportunistic pathogens. This research adds to our understanding of the distribution and spread of antibiotic resistomes in mangrove ecosystems, helping improve ARG risk assessment and management worldwide.}, }
@article {pmid36857575, year = {2023}, author = {Shaffer, M and Borton, MA and Bolduc, B and Faria, JP and Flynn, RM and Ghadermazi, P and Edirisinghe, JN and Wood-Charlson, EM and Miller, CS and Chan, SHJ and Sullivan, MB and Henry, CS and Wrighton, KC}, title = {kb_DRAM: Annotating and functional profiling of genomes with DRAM in KBase.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad110}, pmid = {36857575}, issn = {1367-4811}, abstract = {UNLABELLED: Microbial genome annotation is the process of identifying structural and functional elements in DNA sequences and subsequently attaching biological information to those elements. DRAM is a tool developed to annotate bacterial, archaeal, and viral genomes derived from pure cultures or metagenomes. DRAM goes beyond traditional annotation tools by distilling multiple gene annotations to genome level summaries of functional potential. Despite these benefits, a downside of DRAM is the requirement of large computational resources, which limits its accessibility. Further, it did not integrate with downstream metabolic modeling tools that require genome annotation. To alleviate these constraints, DRAM and the viral counterpart, DRAM-v, are now available and integrated in the freely accessible KBase cyberinfrastructure. With kb_DRAM users can generate DRAM annotations and functional summaries from microbial or viral genomes in a point and click interface, as well as generate genome scale metabolic models from DRAM annotations.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid36533926, year = {2023}, author = {Rogério, F and Baroncelli, R and Cuevas-Fernández, FB and Becerra, S and Crouch, J and Bettiol, W and Azcárate-Peril, MA and Malapi-Wight, M and Ortega, V and Betran, J and Tenuta, A and Dambolena, JS and Esker, PD and Revilla, P and Jackson-Ziems, TA and Hiltbrunner, J and Munkvold, G and Buhiniček, I and Vicente-Villardón, JL and Sukno, SA and Thon, MR}, title = {Population Genomics Provide Insights into the Global Genetic Structure of Colletotrichum graminicola, the Causal Agent of Maize Anthracnose.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0287822}, pmid = {36533926}, issn = {2150-7511}, mesh = {*Zea mays ; Metagenomics ; Ecosystem ; Base Sequence ; *Colletotrichum ; Plant Diseases ; Genetic Variation ; }, abstract = {Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes) C. graminicola can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the C. graminicola population structure. IMPORTANCE Plant pathogens cause significant reductions in yield and crop quality and cause enormous economic losses worldwide. Reducing these losses provides an obvious strategy to increase food production without further degrading natural ecosystems; however, this requires knowledge of the biology and evolution of the pathogens in agroecosystems. We employed a population genomics approach to investigate the genetic diversity and reproductive biology of the maize anthracnose pathogen (Colletotrichum graminicola) in 14 countries. We found that the populations are correlated with their geographical origin and that migration between countries is ongoing, possibly caused by the movement of infected plant material. This result has direct implications for disease management because migration can cause the movement of more virulent and/or fungicide-resistant genotypes. We conclude that genetic recombination is frequent (in contrast to the traditional view of C. graminicola being mainly asexual), which strongly impacts control measures and breeding programs aimed at controlling this disease.}, }
@article {pmid36856771, year = {2023}, author = {Shi, ZJ and Nayfach, S and Pollard, KS}, title = {Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro.}, journal = {STAR protocols}, volume = {4}, number = {1}, pages = {101964}, doi = {10.1016/j.xpro.2022.101964}, pmid = {36856771}, issn = {2666-1667}, abstract = {Genotyping single-nucleotide polymorphisms (SNPs) in microbiomes enables strain-level quantification. In this protocol, we describe a computational pipeline that performs fast and accurate SNP genotyping using metagenomic data. We first demonstrate how to use Maast to catalog SNPs from microbial genomes. Then we use GT-Pro to extract unique SNP-covering k-mers, optimize a data structure for storing these k-mers, and finally perform metagenotyping. For proof of concept, the protocol leverages public whole-genome sequences to metagenotype a synthetic community. For complete details on the use and execution of this protocol, please refer to Shi et al. (2022a)[1] and Shi et al. (2022b).[2].}, }
@article {pmid36856420, year = {2023}, author = {Newman, MR and Sanchez, D and Acosta, AM and Connors, BJ}, title = {Amplicons, Metagenomes, and Metatranscriptomes from Sediment and Water.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0123022}, doi = {10.1128/mra.01230-22}, pmid = {36856420}, issn = {2576-098X}, abstract = {High fecal indicator bacterium (FIB) counts in water have been found to correlate with high sediment FIB counts. To determine the other bacterial populations in common between the two substrates, sediment and water samples from suburban waters known to be impacted by stormwater runoff were examined using next-generation sequencing.}, }
@article {pmid36855809, year = {2023}, author = {Xiong, Q and Li, L and Xiao, Y and He, S and Zhao, J and Lin, X and He, Y and Wang, J and Guo, X and Liang, W and Zuo, X and Ying, C}, title = {The Effect of Inulin-Type Fructans on Plasma Trimethylamine N-Oxide Levels in Peritoneal Dialysis Patients: A Randomized Crossover Trial.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e2200531}, doi = {10.1002/mnfr.202200531}, pmid = {36855809}, issn = {1613-4133}, abstract = {SCOPE: Trimethylamine N-oxide (TMAO), an important proatherogenic uremic toxin, is oxidized by hepatic-flavin monooxygenases from gut microbiome-generated trimethylamine (TMA). The present study aimed to explore whether manipulating the gut microbiota by inulin-type fructans (ITFs) could reduce circulating TMAO levels in peritoneal dialysis patients.<br><br>METHODS AND RESULTS: This was a randomized, double-blind, placebo-controlled, crossover trial with 10&#xa0;g/day ITFs intervention for 3 months in continuous ambulatory peritoneal dialysis patients. The gut microbiome was measured, and TMA-producing gene clusters were annotated using shotgun metagenomic sequencing. Fecal and plasma TMA, plasma TMAO, and daily urine excretion and dialysis removal of TMAO were measured. Finally, 22 participants completed the trial. The daily intake of macronutrients and TMAO precursors was comparable during the prebiotics, washout, and placebo interventions. The ITFs intervention increased the Firmicutes/Bacteroidetes ratio (P = 0.049) of gut microbiome. However, no significant influences were observed on fecal TMA content, circulating TMAO levels, or TMA-producing gene clusters, including choline TMA-lyase (CutC/D), carnitine monooxygenase (CntA/B), and betaine reductase (GrdH).<br><br>CONCLUSIONS: Intervention with 10&#xa0;g/day of ITFs for 3 months was not sufficient to reduce plasma TMAO levels in peritoneal dialysis patients, but it improved the gut microbiome composition. This article is protected by copyright. All rights reserved.}, }
@article {pmid36855218, year = {2023}, author = {Kim, MS and Park, EJ}, title = {Composition and variability of core phyllosphere fungal mycobiota on field-grown broccoli.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {15}, pmid = {36855218}, issn = {2524-6372}, abstract = {BACKGROUND: Fresh vegetables harbor an assemblage of different microorganisms on their surfaces. The phyllosphere microbiota is important for maintaining plant health and managing crop quality before and after harvest. However, the diversity and ecology of fungal communities are largely unexplored in fresh vegetables. This study investigated the phyllosphere mycobiota of field-grown broccoli florets (n = 66) collected from 22 farms across four regions in Korea, using culturing, amplicon sequencing of the internal transcribed spacer region, and microbial network analysis.<br><br>RESULTS: Microbial network analysis identified core genera (Purpureocillium, Filobasidium, Cystofilobasidium, Papiliotrema, Aureobasidium, and unclassified genera of Capnodiales) specific to the broccoli phyllosphere. The composition and network complexity of core and unique populations varied among farming regions, and was associated with local agro-meteorological conditions. The complexity of microbial associations was higher in mature communities than in immature communities, but complexity was lost upon development of plant pathogenic disease. Broccoli mycobiota were classified according to the dominance of Purpurecillium. While Purpurecillium-type microbiota were prevalent in normal samples, Filobasidium-type microbiota were frequently observed in immature, damaged, or postharvest samples.<br><br>CONCLUSIONS: Together, fungal communities were important components of phyllosphere microbiota on fresh vegetables, and have substantial potential for exploitation to enhance and stabilize plant health and growth.}, }
@article {pmid36853748, year = {2023}, author = {Edgeworth, JD}, title = {Respiratory metagenomics: route to routine service.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1097/QCO.0000000000000909}, pmid = {36853748}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: The coronavirus disease 2019 pandemic demonstrated broad utility of pathogen sequencing with rapid methodological progress alongside global distribution of sequencing infrastructure. This review considers implications for now moving clinical metagenomics into routine service, with respiratory metagenomics as the exemplar use-case.<br><br>RECENT FINDINGS: Respiratory metagenomic workflows have completed proof-of-concept, providing organism identification and many genotypic antimicrobial resistance determinants from clinical samples in <6&#x200a;h. This enables rapid escalation or de-escalation of empiric therapy for patient benefit and reducing selection of antimicrobial resistance, with genomic-typing available in the same time-frame. Attention is now focussed on demonstrating clinical, health-economic, accreditation, and regulatory requirements. More fundamentally, pathogen sequencing challenges the traditional culture-orientated time frame of microbiology laboratories, which through automation and centralisation risks becoming increasingly separated from the clinical setting. It presents an alternative future where infection experts are brought together around a single genetic output in an acute timeframe, aligning the microbiology target operating model with the wider human genomic and digital strategy.<br><br>SUMMARY: Pathogen sequencing is a transformational proposition for microbiology laboratories and their infectious diseases, infection control, and public health partners. Healthcare systems that link output from routine clinical metagenomic sequencing, with pandemic and antimicrobial resistance surveillance, will create valuable tools for protecting their population against future infectious diseases threats.}, }
@article {pmid36853049, year = {2023}, author = {Vereecke, N and Zwickl, S and Gumbert, S and Graaf, A and Harder, T and Ritzmann, M and Lillie-Jaschniski, K and Theuns, S and Stadler, J}, title = {Viral and Bacterial Profiles in Endemic Influenza A Virus Infected Swine Herds Using Nanopore Metagenomic Sequencing on Tracheobronchial Swabs.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0009823}, doi = {10.1128/spectrum.00098-23}, pmid = {36853049}, issn = {2165-0497}, abstract = {Swine influenza A virus (swIAV) plays an important role in porcine respiratory infections. In addition to its ability to cause severe disease by itself, it is important in the multietiological porcine respiratory disease complex. Still, to date, no comprehensive diagnostics with which to study polymicrobial infections in detail have been offered. Hence, veterinary practitioners rely on monospecific and costly diagnostics, such as Reverse Transcription quantitative PCR (RT-qPCR), antigen detection, and serology. This prevents the proper understanding of the entire disease context, thereby hampering effective preventive and therapeutic actions. A new, nanopore-based, metagenomic diagnostic platform was applied to study viral and bacterial profiles across 4 age groups on 25 endemic swIAV-infected German farms with respiratory distress in the nursery. Farms were screened for swIAV using RT-qPCR on nasal and tracheobronchial swabs (TBS). TBS samples were pooled per age, prior to metagenomic characterization. The resulting data showed a correlation between the swIAV loads and the normalized reads, supporting a (semi-)quantitative interpretation of the metagenomic data. Interestingly, an in-depth characterization using beta diversity and PERMANOVA analyses allowed for the observation of an age-dependent interplay of known microbial agents. Also, lesser-known microbes, such as porcine polyoma, parainfluenza, and hemagglutinating encephalomyelitis viruses, were observed. Analyses of swIAV incidence and clinical signs showed differing microbial communities, highlighting age-specific observations of various microbes in porcine respiratory disease. In conclusion, nanopore metagenomics were shown to enable a panoramic view on viral and bacterial profiles as well as putative pathogen dynamics in endemic swIAV-infected herds. The results also highlighted the need for better insights into lesser studied agents that are potentially associated with porcine respiratory disease. IMPORTANCE To date, no comprehensive diagnostics for the study of polymicrobial infections that are associated with porcine respiratory disease have been offered. This precludes the proper understanding of the entire disease landscape, thereby hampering effective preventive and therapeutic actions. Compared to the often-costly diagnostic procedures that are applied for the diagnostics of porcine respiratory disease nowadays, a third-generation nanopore sequencing diagnostics workflow presents a cost-efficient and informative tool. This approach offers a panoramic view of microbial agents and contributes to the in-depth observation and characterization of viral and bacterial profiles within the respiratory disease context. While these data allow for the study of age-associated, swIAV-associated, and clinical symptom-associated observations, it also suggests that more effort should be put toward the investigation of coinfections and lesser-known pathogens (e.g., PHEV and PPIV), along with their potential roles in porcine respiratory disease. Overall, this approach will allow veterinary practitioners to tailor treatment and/or management changes on farms in a quicker, more complete, and cost-efficient way.}, }
@article {pmid36853013, year = {2023}, author = {Ren, Y and Hao, L and Liu, J and Wang, P and Ding, Q and Chen, C and Song, Y}, title = {Alterations in the Gut Microbiota in Pregnant Women with Pregestational Type 2 Diabetes Mellitus.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0114622}, doi = {10.1128/msystems.01146-22}, pmid = {36853013}, issn = {2379-5077}, abstract = {Human gut dysbiosis is associated with type 2 diabetes mellitus (T2DM); however, the gut microbiome in pregnant women with pregestational type 2 diabetes mellitus (PGDM) remains unexplored. We investigated the alterations in the gut microbiota composition in pregnant women with or without PGDM. The gut microbiota was examined using 16S rRNA sequencing data of 234 maternal fecal samples that were collected during the first (T1), second (T2), and third (T3) trimesters. The PGDM group presented a reduction in the number of gut bacteria taxonomies as the pregnancies progressed. Linear discriminant analyses revealed that Megamonas, Bacteroides, and Roseburia intestinalis were enriched in the PGDM group, whereas Bacteroides vulgatus, Faecalibacterium prausnitzii, Eubacterium rectale, Bacteroides uniformis, Eubacterium eligens, Subdoligranulum, Bacteroides fragilis, Dialister, Lachnospiraceae, Christensenellaceae R-7, Roseburia inulinivorans, Streptococcus oralis, Prevotella melaninogenica, Neisseria perflava, Bacteroides ovatus, Bacteroides caccae, Veillonella dispar, and Haemophilus parainfluenzae were overrepresented in the control group. Correlation analyses showed that the PGDM-enriched taxa were correlated with higher blood glucose levels during pregnancy, whereas the taxonomic biomarkers of normoglycemic pregnancies exhibited negative correlations with glycemic traits. The microbial networks in the PGDM group comprised weaker microbial interactions than those in the control group. Our study reveals the distinct characteristics of the gut microbiota composition based on gestational ages between normoglycemic and PGDM pregnancies. Further longitudinal research involving women with T2DM at preconception stages and investigations using shotgun metagenomic sequencing should be performed to elucidate the relationships between specific bacterial functions and PGDM metabolic statuses during pregnancy and to identify potential therapeutic targets. IMPORTANCE The incidence of pregestational type 2 diabetes mellitus (PGDM) is increasing, with high rates of serious adverse maternal and neonatal outcomes that are strongly correlated with hyperglycemia. Recent studies have shown that type 2 diabetes mellitus is associated with gut microbial dysbiosis; however, the gut microbiome composition and its associations with the metabolic features of patients with PGDM remain largely unknown. In this study, we investigated the changes in the gut microbiota composition in pregnant women with and without PGDM. We identified differential taxa that may be correlated with maternal metabolic statuses during pregnancy. Additionally, we observed that the number of taxonomic and microbial networks of gut bacteria were distinctly reduced in women with hyperglycemia as their pregnancies progressed. These results extend our understanding of the associations between the gut microbial composition, PGDM-related metabolic changes, and pregnancy outcomes.}, }
@article {pmid36852830, year = {2023}, author = {Oren, A}, title = {Naming new taxa of prokaryotes in the 21st century.}, journal = {Canadian journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1139/cjm-2022-0266}, pmid = {36852830}, issn = {1480-3275}, abstract = {The nomenclature of prokaryotes is regulated by the rules of the International Code of Nomenclature of Prokaryotes (ICNP) and is based on the Linnaean binomial system. The current rules of the Code only cover the nomenclature of the cultivated minority. Proposals to incorporate the uncultivated majority of bacteria and archaea under the rules of the Code were recently rejected by the International Committee on Systematics of Prokaryotes. The provisional rank of Candidatus can be used to name uncultivated prokaryotes whose names cannot be validly published under the rules of the ICNP, but their names can now be validated under the Code of Nomenclature of Prokaryotes Described from Sequence Data (the SeqCode), which was recently established to cover the nomenclature of the uncultivated majority. Metagenomics, single-cell genomics, and high-throughput cultivation techniques have led to a flood of new organisms currently waiting to be named. Automated programs such as GAN and Protologger can assist researchers in naming and describing newly discovered prokaryotes, cultivated as well as uncultivated. However, Latin and Greek skills remain indispensable for proper quality control of names that must meet the standards set by the codes of nomenclature.}, }
@article {pmid36852763, year = {2022}, author = {Sarwal, V and Brito, J and Mangul, S and Koslicki, D}, title = {TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, doi = {10.1093/gigascience/giad008}, pmid = {36852763}, issn = {2047-217X}, abstract = {BACKGROUND: Metagenomic taxonomic profiling aims to predict the identity and relative abundance of taxa in a given whole-genome sequencing metagenomic sample. A recent surge in computational methods that aim to accurately estimate taxonomic profiles, called taxonomic profilers, has motivated community-driven efforts to create standardized benchmarking datasets and platforms, standardized taxonomic profile formats, and a benchmarking platform to assess tool performance. While this standardization is essential, there is currently a lack of tools to visualize the standardized output of the many existing taxonomic profilers. Thus, benchmarking studies rely on a single-value metrics to compare performance of tools and compare to benchmarking datasets. This is one of the major problems in analyzing metagenomic profiling data, since single metrics, such as the F1 score, fail to capture the biological differences between the datasets.<br><br>FINDINGS: Here we report the development of TAMPA (Taxonomic metagenome profiling evaluation), a robust and easy-to-use method that allows scientists to easily interpret and interact with taxonomic profiles produced by the many different taxonomic profiler methods beyond the standard metrics used by the scientific community. We demonstrate the unique ability of TAMPA to generate a novel biological hypothesis by highlighting the taxonomic differences between samples otherwise missed by commonly utilized metrics.<br><br>CONCLUSION: In this study, we show that TAMPA can help visualize the output of taxonomic profilers, enabling biologists to effectively choose the most appropriate profiling method to use on their metagenomics data. TAMPA is available on GitHub, Bioconda, and Galaxy Toolshed at https://github.com/dkoslicki/TAMPA and is released under the MIT license.}, }
@article {pmid36852697, year = {2023}, author = {Saha, A and Gupta, A and Sar, P}, title = {Metagenome based analysis of groundwater from arsenic contaminated sites of West Bengal revealed community diversity and their metabolic potential.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances &amp; environmental engineering}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/10934529.2023.2173919}, pmid = {36852697}, issn = {1532-4117}, abstract = {The study of microbial community in groundwater systems is considered to be essential to improve our understanding of arsenic (As) biogeochemical cycling in aquifers, mainly as it relates to the fate and transport of As. The present study was conducted to determine the microbial community composition and its functional potential using As-contaminated groundwater from part of the Bengal Delta Plain (BDP) in West Bengal, India. Geochemical analyses indicated low to moderate dissolved oxygen (0.42-3.02 mg/L), varying As (2.5-311 µg/L) and Fe (0.19-1.2 mg/L) content, while low concentrations of total organic carbon (TOC), total inorganic carbon (TIC), nitrate, and sulfate were detected. Proteobacteria was the most abundant phylum, while the indiscriminate presence of an array of archaeal phyla, Euryarchaeota, Crenarchaeota, Nanoarchaeota, etc., was noteworthy. The core community members were affiliated to Sideroxydans, Acidovorax, Pseudoxanthomonas, Brevundimonas, etc. However, diversity assessed over multiple seasons indicated a shift from Sideroxydans to Pseudomonas or Brevundimonas dominant community, suggestive of microbial response to seasonally fluctuating geochemical stimuli. Taxonomy-based functional potential showed prospects for As biotransformation, methanogenesis, sulfate respiration, denitrification, etc. Thus, this study strengthened existing reports from this region by capturing the less abundant or difficult-to-culture taxa collectively forming a major fraction of the microbial community.}, }
@article {pmid36851800, year = {2023}, author = {Ibañez-Lligoña, M and Colomer-Castell, S and González-Sánchez, A and Gregori, J and Campos, C and Garcia-Cehic, D and Andrés, C and Piñana, M and Pumarola, T and Rodríguez-Frias, F and Antón, A and Quer, J}, title = {Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851800}, issn = {1999-4915}, abstract = {Epidemics and pandemics have occurred since the beginning of time, resulting in millions of deaths. Many such disease outbreaks are caused by viruses. Some viruses, particularly RNA viruses, are characterized by their high genetic variability, and this can affect certain phenotypic features: tropism, antigenicity, and susceptibility to antiviral drugs, vaccines, and the host immune response. The best strategy to face the emergence of new infectious genomes is prompt identification. However, currently available diagnostic tests are often limited for detecting new agents. High-throughput next-generation sequencing technologies based on metagenomics may be the solution to detect new infectious genomes and properly diagnose certain diseases. Metagenomic techniques enable the identification and characterization of disease-causing agents, but they require a large amount of genetic material and involve complex bioinformatic analyses. A wide variety of analytical tools can be used in the quality control and pre-processing of metagenomic data, filtering of untargeted sequences, assembly and quality control of reads, and taxonomic profiling of sequences to identify new viruses and ones that have been sequenced and uploaded to dedicated databases. Although there have been huge advances in the field of metagenomics, there is still a lack of consensus about which of the various approaches should be used for specific data analysis tasks. In this review, we provide some background on the study of viral infections, describe the contribution of metagenomics to this field, and place special emphasis on the bioinformatic tools (with their capabilities and limitations) available for use in metagenomic analyses of viral pathogens.}, }
@article {pmid36851794, year = {2023}, author = {Dart, E and Fuhrman, JA and Ahlgren, NA}, title = {Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851794}, issn = {1999-4915}, abstract = {Cyanophages exert important top-down controls on their cyanobacteria hosts; however, concurrent analysis of both phage and host populations is needed to better assess phage-host interaction models. We analyzed picocyanobacteria Prochlorococcus and Synechococcus and T4-like cyanophage communities in Pacific Ocean surface waters using five years of monthly viral and cellular fraction metagenomes. Cyanophage communities contained thousands of mostly low-abundance (<2% relative abundance) species with varying temporal dynamics, categorized as seasonally recurring or non-seasonal and occurring persistently, occasionally, or sporadically (detected in ≥85%, 15-85%, or <15% of samples, respectively). Viromes contained mostly seasonal and persistent phages (~40% each), while cellular fraction metagenomes had mostly sporadic species (~50%), reflecting that these sample sets capture different steps of the infection cycle-virions from prior infections or within currently infected cells, respectively. Two groups of seasonal phages correlated to Synechococcus or Prochlorococcus were abundant in spring/summer or fall/winter, respectively. Cyanophages likely have a strong influence on the host community structure, as their communities explained up to 32% of host community variation. These results support how both seasonally recurrent and apparent stochastic processes, likely determined by host availability and different host-range strategies among phages, are critical to phage-host interactions and dynamics, consistent with both the Kill-the-Winner and the Bank models.}, }
@article {pmid36851780, year = {2023}, author = {Krasnikov, N and Yuzhakov, A and Aliper, T and Gulyukin, A}, title = {Metagenomic Approach Reveals the Second Subtype of PRRSV-1 in a Pathogen Spectrum during a Clinical Outbreak with High Mortality in Western Siberia, Russia.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851780}, issn = {1999-4915}, abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) has a significant economic impact on pig farming worldwide by causing reproductive problems and affecting the respiratory systems of swine. In Eastern Europe, PRRSV-1 strains are characterized by high genetic variability, and pathogenicity differs among all known subtypes. This case study describes the detection of a wide pathogen spectrum, including the second subtype PRRSV-1, with a high mortality rate among nursery piglets (23.8%). This study was conducted at a farrow-to-finish farm in the Western Siberia region of Russia. Clinical symptoms included apathy, sneezing, and an elevation in body temperature, and during the autopsy, degenerative lesions in different tissues were observed. Moreover, 1.5 percent of the affected animals displayed clinical signs of the central nervous system and were characterized by polyserositis. Nasal swabs from diseased piglets and various tissue swabs from deceased animals were studied. For diagnostics, the nanopore sequencing method was applied. All the samples tested positive for PRRSV, and a more detailed analysis defined it as a second subtype of PRRSV-1. The results, along with the clinical picture, showed a complex disease etiology with the dominant role of PRRSV-1 and were informative about the high pathogenicity of the subtype in question under field conditions.}, }
@article {pmid36851669, year = {2023}, author = {Ambrose, RK and Blakebrough-Hall, C and Gravel, JL and Gonzalez, LA and Mahony, TJ}, title = {Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851669}, issn = {1999-4915}, abstract = {Bovine respiratory disease (BRD) is a major health problem within the global cattle industry. This disease has a complex aetiology, with viruses playing an integral role. In this study, metagenomics was used to sequence viral nucleic acids in the nasal swabs of BRD-affected cattle. The viruses detected included those that are well known for their association with BRD in Australia (bovine viral diarrhoea virus 1), as well as viruses known to be present but not fully characterised (bovine coronavirus) and viruses that have not been reported in BRD-affected cattle in Australia (bovine rhinitis, bovine influenza D, and bovine nidovirus). The nasal swabs from a case-control study were subsequently tested for 10 viruses, and the presence of at least one virus was found to be significantly associated with BRD. Some of the more recently detected viruses had inconsistent associations with BRD. Full genome sequences for bovine coronavirus, a virus increasingly associated with BRD, and bovine nidovirus were completed. Both viruses belong to the Coronaviridae family, which are frequently associated with disease in mammals. This study has provided greater insights into the viral pathogens associated with BRD and highlighted the need for further studies to more precisely elucidate the roles viruses play in BRD.}, }
@article {pmid36851645, year = {2023}, author = {Plyusnin, I and Vapalahti, O and Sironen, T and Kant, R and Smura, T}, title = {Enhanced Viral Metagenomics with Lazypipe 2.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851645}, issn = {1999-4915}, abstract = {Viruses are the main agents causing emerging and re-emerging infectious diseases. It is therefore important to screen for and detect them and uncover the evolutionary processes that support their ability to jump species boundaries and establish themselves in new hosts. Metagenomic next-generation sequencing (mNGS) is a high-throughput, impartial technology that has enabled virologists to detect either known or novel, divergent viruses from clinical, animal, wildlife and environmental samples, with little a priori assumptions. mNGS is heavily dependent on bioinformatic analysis, with an emerging demand for integrated bioinformatic workflows. Here, we present Lazypipe 2, an updated mNGS pipeline with, as compared to Lazypipe1, significant improvements in code stability and transparency, with added functionality and support for new software components. We also present extensive benchmarking results, including evaluation of a novel canine simulated metagenome, precision and recall of virus detection at varying sequencing depth, and a low to extremely low proportion of viral genetic material. Additionally, we report accuracy of virus detection with two strategies: homology searches using nucleotide or amino acid sequences. We show that Lazypipe 2 with nucleotide-based annotation approaches near perfect detection for eukaryotic viruses and, in terms of accuracy, outperforms the compared pipelines. We also discuss the importance of homology searches with amino acid sequences for the detection of highly divergent novel viruses.}, }
@article {pmid36851634, year = {2023}, author = {Miller-Ensminger, T and Johnson, G and Banerjee, S and Putonti, C}, title = {When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851634}, issn = {1999-4915}, abstract = {High-throughput sequencing of microbial communities has uncovered a large, diverse population of phages. Frequently, phages found are integrated into their bacterial host genome. Distinguishing between phages in their integrated (lysogenic) and unintegrated (lytic) stage can provide insight into how phages shape bacterial communities. Here we present the Prophage Induction Estimator (PIE) to identify induced phages in genomic and metagenomic sequences. PIE takes raw sequencing reads and phage sequence predictions, performs read quality control, read assembly, and calculation of phage and non-phage sequence abundance and completeness. The distribution of abundances for non-phage sequences is used to predict induced phages with statistical confidence. In silico tests were conducted to benchmark this tool finding that PIE can detect induction events as well as phages with a relatively small burst size (10×). We then examined isolate genome sequencing data as well as a mock community and urinary metagenome data sets and found instances of induced phages in all three data sets. The flexibility of this software enables users to easily include phage predictions from their preferred tool of choice or phage sequences of interest. Thus, genomic and metagenomic sequencing now not only provides a means for discovering and identifying phage sequences but also the detection of induced prophages.}, }
@article {pmid36851611, year = {2023}, author = {Starchevskaya, M and Kamanova, E and Vyatkin, Y and Tregubchak, T and Bauer, T and Bodnev, S and Rotskaya, U and Polenogova, O and Kryukov, V and Antonets, D}, title = {The Metagenomic Analysis of Viral Diversity in Colorado Potato Beetle Public NGS Data.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851611}, issn = {1999-4915}, abstract = {The Colorado potato beetle (CPB) is one of the most serious insect pests due to its high ecological plasticity and ability to rapidly develop resistance to insecticides. The use of biological insecticides based on viruses is a promising approach to control insect pests, but the information on viruses which infect leaf feeding beetles is scarce. We performed a metagenomic analysis of 297 CPB genomic and transcriptomic samples from the public National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) database. The reads that were not aligned to the reference genome were assembled with metaSPAdes, and 13314 selected contigs were analyzed with BLAST tools. The contigs and non-aligned reads were also analyzed with Kraken2 software. A total of 3137 virus-positive contigs were attributed to different viruses belonging to 6 types, 17 orders, and 32 families, matching over 97 viral species. The annotated sequences can be divided into several groups: those that are homologous to genetic sequences of insect viruses (Adintoviridae, Ascoviridae, Baculoviridae, Dicistroviridae, Chuviridae, Hytrosaviridae, Iflaviridae, Iridoviridae, Nimaviridae, Nudiviridae, Phasmaviridae, Picornaviridae, Polydnaviriformidae, Xinmoviridae etc.), plant viruses (Betaflexiviridae, Bromoviridae, Kitaviridae, Potyviridae), and endogenous retroviral elements (Retroviridae, Metaviridae). Additionally, the full-length genomes and near-full length genome sequences of several viruses were assembled. We also found sequences belonging to Bracoviriform viruses and, for the first time, experimentally validated the presence of bracoviral genetic fragments in the CPB genome. Our work represents the first attempt to discover the viral genetic material in CPB samples, and we hope that further studies will help to identify new viruses to extend the arsenal of biopesticides against CPB.}, }
@article {pmid36850017, year = {2023}, author = {Theelen, MJP and Luiken, REC and Wagenaar, JA and Sloet van Oldruitenborgh-Oosterbaan, MM and Rossen, JWA and Schaafstra, FJWC and van Doorn, DA and Zomer, AL}, title = {Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {33}, pmid = {36850017}, issn = {2049-2618}, abstract = {BACKGROUND: Hospitalisation and antimicrobial treatment are common in horses and significantly impact the intestinal microbiota. Antimicrobial treatment might also increase levels of resistant bacteria in faeces, which could spread to other ecological compartments, such as the environment, other animals and humans. In this study, we aimed to characterise the short- and long-term effects of transportation, hospitalisation and trimethoprim-sulfadiazine (TMS) administration on the faecal microbiota and resistome of healthy equids.<br><br>METHODS: In a longitudinal experimental study design, in which the ponies served as their own control, faecal samples were collected from six healthy Welsh ponies at the farm (D0-D13-1), immediately following transportation to the hospital (D13-2), during 7 days of hospitalisation without treatment (D14-D21), during 5 days of oral TMS treatment (D22-D26) and after discharge from the hospital up to 6 months later (D27-D211). After DNA extraction, 16S rRNA gene sequencing was performed on all samples. For resistome analysis, shotgun metagenomic sequencing was performed on selected samples.<br><br>RESULTS: Hospitalisation without antimicrobial treatment did not significantly affect microbiota composition. Oral TMS treatment reduced alpha-diversity significantly. Kiritimatiellaeota, Fibrobacteres and Verrucomicrobia significantly decreased in relative abundance, whereas Firmicutes increased. The faecal microbiota composition gradually recovered after discontinuation of TMS treatment and discharge from the hospital and, after 2 weeks, was more similar to pre-treatment composition than to composition during TMS treatment. Six months later, however, microbiota composition still differed significantly from that at the start of the study and Spirochaetes and Verrucomicrobia were less abundant. TMS administration led to a significant (up to 32-fold) and rapid increase in the relative abundance of resistance genes sul2, tetQ, ant6-1a, and aph(3")-lb. lnuC significantly decreased directly after treatment. Resistance genes sul2 (15-fold) and tetQ (six-fold) remained significantly increased 6 months later.<br><br>CONCLUSIONS: Oral treatment with TMS has a rapid and long-lasting effect on faecal microbiota composition and resistome, making the equine hindgut a reservoir and potential source of resistant bacteria posing a risk to animal and human health through transmission. These findings support the judicious use of antimicrobials to minimise long-term faecal presence, excretion and the spread of antimicrobial resistance in the environment. Video Abstract.}, }
@article {pmid36849099, year = {2023}, author = {Qiao, X and Fu, C and Chen, Y and Fang, F and Zhang, Y and Ding, L and Yang, K and Pan, B and Xu, N and Yu, K and Tao, H and Zhang, L}, title = {Molecular insights into enhanced nitrogen removal induced by trace fluoroquinolone antibiotics in an anammox system.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {128784}, doi = {10.1016/j.biortech.2023.128784}, pmid = {36849099}, issn = {1873-2976}, abstract = {It has been widely reported that fluoroquinolones (FQs) can affect the anaerobic ammonium oxidization (anammox) microorganisms, which interferes with the performance of nitrogen removal from wastewater. However, the metabolic mechanism of anammox microorganisms responding to FQs has rarely been explored. In this study, it was found that 20 μg/L FQs promoted the nitrogen removal performance of anammox microorganisms in batch exposure assays, and 36-51% of FQs were removed simultaneously. Combined metabolomics and genome-resolved metagenomic analysis revealed up-regulated carbon fixation in anammox bacteria (AnAOB), while purine and pyrimidine metabolism, protein generation and transmembrane transport were enhanced in AnAOB and symbiotic bacteria by 20 μg/L FQs. Consequently, hydrazine dehydrogenation, nitrite reduction, and ammonium assimilation were bolstered, improving the nitrogen removal efficiency of the anammox system. These results revealed the potential roles of specific microorganisms in response to emerging FQs and provided further information for practical application of anammox technology in wastewater treatment.}, }
@article {pmid36848852, year = {2023}, author = {Liang, Y and Zhou, X and Wu, Y and Wu, Y and Zeng, X and Yu, Z and Peng, P}, title = {Meta-omics elucidates key degraders in a bacterial tris(2-butoxyethyl) phosphate (TBOEP)-degrading enrichment culture.}, journal = {Water research}, volume = {233}, number = {}, pages = {119774}, doi = {10.1016/j.watres.2023.119774}, pmid = {36848852}, issn = {1879-2448}, abstract = {Organophosphate esters (OPEs) are emerging contaminants of growing concern, and there is limited information about the bacterial transformation of OPEs. In this study, we investigated the biotransformation of tris(2-butoxyethyl) phosphate (TBOEP), a frequently detected alkyl-OPE by a bacterial enrichment culture under aerobic conditions. The enrichment culture degraded 5 mg/L TBOEP following the first-order kinetics with a reaction rate constant of 0.314 h[-1]. TBOEP was mainly degraded via ether bond cleavage, evidenced by the production of bis(2-butoxyethyl) hydroxyethyl phosphate, 2-butoxyethyl bis(2-hydroxyethyl) phosphate, and 2-butoxyethyl (2-hydroxyethyl) hydrogen phosphate. Other transformation pathways include terminal oxidation of the butoxyethyl group and phosphoester bond hydrolysis. Metagenomic sequencing generated 14 metagenome-assembled genomes (MAGs), showing that the enrichment culture primarily consisted of Gammaproteobacteria, Bacteroidota, Myxococcota, and Actinobacteriota. One MAG assigned to Rhodocuccus ruber strain C1 was the most active in the community, showing upregulation of various monooxygenase, dehydrogenase, and phosphoesterase genes throughout the degradation process, and thus was identified as the key degrader of TBOEP and the metabolites. Another MAG affiliated with Ottowia mainly contributed to TBOEP hydroxylation. Our results provided a comprehensive understanding of the bacterial TBOEP degradation at community level.}, }
@article {pmid36848210, year = {2023}, author = {Rojas-Gätjens, D and Avey-Arroyo, J and Chaverri, P and Rojas-Jimenez, K and Chavarría, M}, title = {Differences in fungal communities in the fur of two- and three-toed sloths revealed by ITS metabarcoding.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {2}, pages = {}, doi = {10.1099/mic.0.001309}, pmid = {36848210}, issn = {1465-2080}, abstract = {Sloths have dense fur on which insects, algae, bacteria and fungi coexist. Previous studies using cultivation-dependent methods and 18S rRNA sequencing revealed that the fungal communities in their furs comprise members of the phyla Ascomycota and Basidiomycota. In this note, we increase the resolution and knowledge of the mycobiome inhabiting the fur of the two- (Choloepus hoffmanni) and three-toed (Bradypus variegatus) sloths. Targeted amplicon metagenomic analysis of ITS2 nrDNA sequences obtained from 10 individuals of each species inhabiting the same site revealed significant differences in the structure of their fungal communities and also in the alpha-diversity estimators. The results suggest a specialization by host species and that the host effect is stronger than that of sex, age and animal weight. Capnodiales were the dominant order in sloths' fur and Cladosporium and Neodevriesia were the most abundant genera in Bradypus and Choloepus, respectively. The fungal communities suggest that the green algae that inhabit the fur of sloths possibly live lichenized with Ascomycota fungal species. The data shown in this note offer a more detailed view of the fungal content in the fur of these extraordinary animals and could help explain other mutualistic relationships in this complex ecosystem.}, }
@article {pmid36847914, year = {2023}, author = {Jin, X and Wang, JK and Wang, Q}, title = {Microbial β-glucanases: production, properties, and engineering.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {39}, number = {4}, pages = {106}, pmid = {36847914}, issn = {1573-0972}, abstract = {Lignocellulosic biomass, which mainly consists of cellulose and hemicellulose, is the most abundant renewable biopolymer on earth. β-Glucanases are glycoside hydrolases (GHs) that hydrolyze β-glucan, one of the dominant components of the plant cell wall, into cello-oligosaccharides and glucose. Among them, endo-β-1,4-glucanase (EC 3.2.1.4), exo-glucanase/cellobiohydrolase (EC 3.2.1.91), and β-glucosidase (EC 3.2.1.21) play critical roles in the digestion of glucan-like substrates. β-Glucanases have attracted considerable interest within the scientific community due to their applications in the feed, food, and textile industries. In the past decade, there has been considerable progress in the discovery, production, and characterization of novel β-glucanases. Advances in the development of next-generation sequencing techniques, including metagenomics and metatranscriptomics, have unveiled novel β-glucanases isolated from the gastrointestinal microbiota. The study of β-glucanases is beneficial for research and development of commercial products. In this study, we review the classification, properties, and engineering of β-glucanases.}, }
@article {pmid36847735, year = {2023}, author = {Saraiva, JP and Bartholomäus, A and Toscan, RB and Baldrian, P and da Rocha, UN}, title = {Recovery of 197 Eukaryotic bins reveals major challenges for Eukaryote genome reconstruction from terrestrial metagenomes.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13776}, pmid = {36847735}, issn = {1755-0998}, abstract = {As most Eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recovering Prokaryotic genomes have become common in genome biology, few studies have tackled the recovery of Eukaryotic genomes from metagenomes. This study assessed the reconstruction of microbial eukaryotic genomes using 6000 metagenomes from terrestrial and some transition environments using the EukRep pipeline. Only 215 metagenomic libraries yielded eukaryotic bins. From a total of 447 eukaryotic bins recovered 197 were classified at the phylum level. Streptophytes and fungi were the most represented clades with 83 and 73 bins, respectively. More than 78% of the obtained eukaryotic bins were recovered from samples whose biomes were classified as host-associated, aquatic, and anthropogenic terrestrial. However, only 93 bins were taxonomically assigned at the genus level and 17 bins at the species level. Completeness and contamination estimates were obtained for a total of 193 bins and consisted of 44.64% (σ=27.41%) and 3.97% (σ=6.53%), respectively. Micromonas commoda was the most frequent taxon found while Saccharomyces cerevisiae presented the highest completeness, probably because more reference genomes are available. Current measures of completeness are based on the presence of single-copy genes. However, mapping of the contigs from the recovered eukaryotic bins to the chromosomes of the reference genomes showed many gaps, suggesting that completeness measures should also include chromosome coverage. Recovering eukaryotic genomes will benefit significantly from long-read sequencing, development of tools for dealing with repeat-rich genomes, and improved reference genomes databases.}, }
@article {pmid36847620, year = {2023}, author = {Gu, BH and Choi, JP and Park, T and Kim, AS and Jung, HY and Choi, DY and Lee, SJ and Chang, YS and Kim, M and Park, HK}, title = {Adult asthma with symptomatic eosinophilic inflammation is accompanied by alteration in gut microbiome.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.15691}, pmid = {36847620}, issn = {1398-9995}, abstract = {BACKGROUND: Accumulating evidence suggests that the gut microbiome is associated with asthma. However, altered gut microbiome in adult asthma is not yet well established. We aimed to investigate the gut microbiome profiles of adult asthmatic patients with symptomatic eosinophilic inflammation.<br><br>METHODS: The 16s rRNA gene metagenomic analysis of feces in the symptomatic eosinophilic asthma group (EA, N=28) was compared with the healthy control (HC, N=18) and the chronic cough control (CC, N=13). A correlation analysis between individual taxa and clinical markers was performed within the EA group. Changes in the gut microbiome were examined in patients with significant symptom improvement in the EA group.<br><br>RESULTS: The relative abundances of Lachnospiraceae and Oscillospiraceae significantly decreased and Bacteroidetes increased in the EA group. Within EA group, Lachnospiraceae was negatively correlated with indicators of type 2 inflammation and lung function decline. Enterobacteriaceae and Prevotella was positively associated with type 2 inflammation and lung function decline, respectively. The abundance of predicted genes associated with amino acid metabolism and secondary bile acid biosynthesis was diminished in the EA group. These functional gene family alterations could be related to gut permeability, and the serum lipopolysaccharide concentration was actually high in the EA group. EA patients with symptom improvement after 1 month did not show a significant change in the gut microbiome.<br><br>CONCLUSIONS: Symptomatic eosinophilic adult asthma patients showed altered the gut microbiome composition. Specifically, a decrease in commensal clostridia was observed, and a decrease in Lachnospiraceae was correlated with blood eosinophilia and lung function decline.}, }
@article {pmid36847544, year = {2023}, author = {Mitra, A and Caron, DA and Faure, E and Flynn, KJ and Gonçalves Leles, S and Hansen, PJ and McManus, GB and Not, F and do Rosario Gomes, H and Santoferrara, L and Stoecker, DK and Tillmann, U}, title = {The Mixoplankton Database - diversity of photo-phago-trophic plankton in form, function and distribution across the global ocean.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {e12972}, doi = {10.1111/jeu.12972}, pmid = {36847544}, issn = {1550-7408}, abstract = {Protist plankton are major members of open-water marine food webs. Traditionally divided between phototrophic phytoplankton and phagotrophic zooplankton, recent research shows many actually combine phototrophy and phagotrophy in the one cell; these protists are the 'mixoplankton'. Under the mixoplankton paradigm, 'phytoplankton' are incapable of phagotrophy (diatoms being exemplars), while 'zooplankton' are incapable of phototrophy. This revision restructures marine food webs, from regional to global levels. Here we present the first comprehensive database of marine mixoplankton, bringing together extant knowledge of the identity, allometry, physiology and trophic interactivity of these organisms. This Mixoplankton Database (MDB) will aid researchers that confront difficulties in characterizing life traits of protist plankton, and it will benefit modellers needing to better appreciate ecology of these organisms with their complex functional and allometric predator-prey interactions. The MDB also identifies knowledge gaps, including the need to better understand, for different mixoplankton functional types, sources of nutrition (use of nitrate, prey types and nutritional states), and to obtain vital rates (e.g., growth, photosynthesis, ingestion, factors affecting photo' versus phago' -trophy). It is now possible to revisit and re-classify protistan 'phytoplankton' and 'zooplankton' in extant databases of plankton life forms so as to clarify their roles in marine ecosystems.}, }
@article {pmid36847515, year = {2023}, author = {Gauthier, NPG and Chorlton, SD and Krajden, M and Manges, AR}, title = {Agnostic Sequencing for Detection of Viral Pathogens.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0011922}, doi = {10.1128/cmr.00119-22}, pmid = {36847515}, issn = {1098-6618}, abstract = {The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.}, }
@article {pmid36846796, year = {2023}, author = {Feng, J and Lin, T and Mihalca, AD and Niu, Q and Oosthuizen, MC}, title = {Editorial: Coinfections of Lyme disease and other tick-borne diseases.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1140545}, doi = {10.3389/fmicb.2023.1140545}, pmid = {36846796}, issn = {1664-302X}, }
@article {pmid36846795, year = {2023}, author = {Nan, Q and Ye, Y and Tao, Y and Jiang, X and Miao, Y and Jia, J and Miao, J}, title = {Alterations in metabolome and microbiome signatures provide clues to the role of antimicrobial peptide KT2 in ulcerative colitis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1027658}, pmid = {36846795}, issn = {1664-302X}, abstract = {INTRODUCTION: Ulcerative colitis (UC) is an inflammatory disease of the intestinal tract with unknown etiology. Both genetic and environmental factors are involved in the occurrence and development of UC. Understanding changes in the microbiome and metabolome of the intestinal tract is crucial for the clinical management and treatment of UC.<br><br>METHODS: Here, we performed metabolomic and metagenomic profiling of fecal samples from healthy control mice (HC group), DSS (Dextran Sulfate Sodium Salt) -induced UC mice (DSS group), and KT2-treated UC mice (KT2 group).<br><br>RESULTS AND DISCUSSION: In total, 51 metabolites were identified after UC induction, enriched in phenylalanine metabolism, while 27 metabolites were identified after KT2 treatment, enriched in histidine metabolism and bile acid biosynthesis. Fecal microbiome analysis revealed significant differences in nine bacterial species associated with the course of UC, including Bacteroides, Odoribacter, and Burkholderiales, which were correlated with aggravated UC, and Anaerotruncus, Lachnospiraceae, which were correlated with alleviated UC. We also identified a disease-associated network connecting the above bacterial species with UC-associated metabolites, including palmitoyl sphingomyelin, deoxycholic acid, biliverdin, and palmitoleic acid. In conclusion, our results indicated that Anaerotruncus, Lachnospiraceae, and Mucispirillum were protective species against DSS-induced UC in mice. The fecal microbiomes and metabolomes differed significantly among the UC mice and KT2-treated and healthy-control mice, providing potential evidence for the discovery of biomarkers of UC.}, }
@article {pmid36846781, year = {2023}, author = {Fu, L and Lai, S and Zhou, Z and Chen, Z and Cheng, L}, title = {Seasonal variation of microbial community and methane metabolism in coalbed water in the Erlian Basin, China.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1114201}, pmid = {36846781}, issn = {1664-302X}, abstract = {Coalbed water is a semi-open system connecting underground coalbeds with the external environment. Microorganisms in coalbed water play an important role in coal biogasification and the carbon cycle. The community assemblages of microorganisms in such a dynamic system are not well understood. Here, we used high-throughput sequencing and metagenomic analysis to investigate microbial community structure and identify the potential functional microorganisms involved in methane metabolism in coalbed water in the Erlian Basin, a preferred low-rank coal bed methane (CBM) exploration and research area in China. The results showed that there were differences in the responses of bacteria and archaea to seasonal variation. Bacterial community structure was affected by seasonal variation but archaea was not. Methane oxidation metabolism dominated by Methylomonas and methanogenesis metabolism dominated by Methanobacterium may exist simultaneously in coalbed water.}, }
@article {pmid36846768, year = {2023}, author = {Min, Z and Yang, L and Hu, Y and Huang, R}, title = {Oral microbiota dysbiosis accelerates the development and onset of mucositis and oral ulcers.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1061032}, pmid = {36846768}, issn = {1664-302X}, abstract = {With the rapid development of metagenomic high-throughput sequencing technology, more and more oral mucosal diseases have been proven to be associated with oral microbiota shifts or dysbiosis. The commensal oral microbiota can greatly influence the colonization and resistance of pathogenic microorganisms and induce primary immunity. Once dysbiosis occurs, it can lead to damage to oral mucosal epithelial defense, thus accelerating the pathological process. As common oral mucosal diseases, oral mucositis and ulcers seriously affect patients' prognosis and quality of life. However, from the microbiota perspective, the etiologies, specific alterations of oral flora, pathogenic changes, and therapy for microbiota are still lacking in a comprehensive overview. This review makes a retrospective summary of the above problems, dialectically based on oral microecology, to provide a new perspective on oral mucosal lesions management and aims at improving patients' quality of life.}, }
@article {pmid36846760, year = {2023}, author = {Vuillemin, A}, title = {Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1101902}, pmid = {36846760}, issn = {1664-302X}, abstract = {Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes, and stable-isotope probing incubations from the water column and subseafloor of the Benguela upwelling system. The taxonomic composition of 16S rRNA genes and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity toward mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria, and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification is fueled by fixed and organic nitrogen dissolved in dysoxic waters, and prevails over canonical denitrification and anaerobic oxidation of ammonia when the Namibian coastal waters and sediment-water interface on the shelf are ventilated by lateral currents during austral winter.}, }
@article {pmid36846759, year = {2023}, author = {Wei, TS and Gao, ZM and Gong, L and Li, QM and Zhou, YL and Chen, HG and He, LS and Wang, Y}, title = {Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1078171}, pmid = {36846759}, issn = {1664-302X}, abstract = {Sponges are widely distributed in the global ocean and harbor diverse symbiotic microbes with mutualistic relationships. However, sponge symbionts in the deep sea remain poorly studied at the genome level. Here, we report a new glass sponge species of the genus Bathydorus and provide a genome-centric view of its microbiome. We obtained 14 high-quality prokaryotic metagenome-assembled genomes (MAGs) affiliated with the phyla Nitrososphaerota, Pseudomonadota, Nitrospirota, Bdellovibrionota, SAR324, Bacteroidota, and Patescibacteria. In total, 13 of these MAGs probably represent new species, suggesting the high novelty of the deep-sea glass sponge microbiome. An ammonia-oxidizing Nitrososphaerota MAG B01, which accounted for up to 70% of the metagenome reads, dominated the sponge microbiomes. The B01 genome had a highly complex CRISPR array, which likely represents an advantageous evolution toward a symbiotic lifestyle and forceful ability to defend against phages. A sulfur-oxidizing Gammaproteobacteria species was the second most dominant symbiont, and a nitrite-oxidizing Nitrospirota species could also be detected, but with lower relative abundance. Bdellovibrio species represented by two MAGs, B11 and B12, were first reported as potential predatory symbionts in deep-sea glass sponges and have undergone dramatic genome reduction. Comprehensive functional analysis indicated that most of the sponge symbionts encoded CRISPR-Cas systems and eukaryotic-like proteins for symbiotic interactions with the host. Metabolic reconstruction further illustrated their essential roles in carbon, nitrogen, and sulfur cycles. In addition, diverse putative phages were identified from the sponge metagenomes. Our study expands the knowledge of microbial diversity, evolutionary adaption, and metabolic complementarity in deep-sea glass sponges.}, }
@article {pmid36846685, year = {2023}, author = {Rüstemoğlu, M and Erkan, ME and Cengiz, G and Hajyzadeh, M}, title = {Bacterial metagenome profiling of hand-made herby cheese samples utilizing high-throughput sequencing to detect geographical indication and marketing potential.}, journal = {Heliyon}, volume = {9}, number = {2}, pages = {e13334}, pmid = {36846685}, issn = {2405-8440}, abstract = {Food safety has been a major concern for consumers. Origin of food products matter for consumers such that the quality, reputation, or other special characteristics can be attributed essentially to that origin. While a geographical indication informs consumers for the origin of the product, it develops a competitive advantage for the markets. To detect distinguishing features of dairy products, the microbial composition of its microbiota is one of the emerging areas of interest. Utilizing novel approaches such as Next Generation Sequencing (NGS) technology to decipher the genetic code of 16s rRNA genes to characterize the bacterial population is widely applied. The bacterial microbiota of the herby cheese samples which were collected from Şırnak province in the South Eastern region of Turkey was examined by an NGS approach for purpose of finding geographical indication possibilities. In brief, Firmicutes is the dominant phyla where Lactobacillaceae and Streptococcaceae are abundant families across the analyzed herby cheese microbiota. The most prominent species is Companilactobacillus ginsenosidimutans detected as the dominant member of the bacterial consortia in 16 herby cheese samples. Another remarkable finding reported here is the Weissella jogaejeotgali which was detected in 15 cheese samples. Albeit the abundance of Levilactobacillus koreensis is low at the microbiome level it was identified in four herby cheese samples. As expected, lactic acid bacteria such as Lactobacillus delbrueckii, Lactococcus raffinolactis and Tetragenococcus halophilus were also identified. On the other hand, bacterial diversity and microbial composition among cheese samples are not significantly affected by mixing different herbs on the manufacturing of herby cheeses. To the best of our knowledge, C. ginsenosidimutans, W. jogaejeotgali and L. koreensis are identified and reported for the first time in a dairy product and the bacterial richness and evenness of herby cheese are higher than those of most other cheeses. These findings make the cheeses in the geography where the samples were produced more valuable and provide opportunities for them to receive geographical indications. Thus, it will create added value while marketing the products.}, }
@article {pmid36846335, year = {2023}, author = {He, L and Yang, H and Liu, S and Liang, W and Zhou, Z and Long, J and Wu, J}, title = {Physiological analysis of severe chlamydia psittaci pneumonia and clinical diagnosis after doxycycline-based treatment.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1132724}, pmid = {36846335}, issn = {1664-042X}, abstract = {Objective: To describe the clinical spectrum of severe Chlamydia psittaci pneumonia in order to understand the disease better. Methods: Retrospective analysis was made on 31 patients with severe Chlamydia psittaci pneumonia diagnosed in ICU by next-generation sequencing of metagenome Metagenomic next-generation sequencing(mNGS) from January 2019-November 2022, including clinical characteristics, laboratory examination results, imaging characteristics, treatment, and prognosis. Results: We included 31 patients with severe Chlamydia psittaci pneumonia, 15 of whom had a history of virus exposure. There were 12 cases with multiple bacterial infections, and the common symptoms included fever (31/31,100%), dyspnea (31/31, 100%), cough (22/31, 71.0%), and myalgia (20/31, 64.5%). Laboratory data showed that white blood cells were average or slightly increased, but the levels of C-reactive protein and neutrophils were high. CT findings of the lung were consolidation (19/31, 61.3%) and pleural effusion (11/31, 35.5%). Only one lobe was involved in 11 patients (35.5%). Before diagnosis, 22 patients (71.0%) did not have atypical pathogens in their antimicrobial regimen. After diagnosis, 19 patients (61.3%) received single drug treatment, of which doxycycline or moxifloxacin were the most commonly used drugs. Among 31 patients, three died, nine improved, and nineteen were cured. Conclusion: The clinical manifestations of severe Chlamydia psittaci pneumonia are non-specific. The application of mNGS can improve the diagnostic accuracy of Chlamydia psittaci pneumonia, reduce the unnecessary use of antibiotics, and shorten the course of the disease. Doxycycline-based treatment is effective for severe chlamydia psittaci pneumonia, but it is necessary to understand the secondary bacterial infection and other complications in the course of the disease.}, }
@article {pmid36846017, year = {2023}, author = {Huang, Y and Zheng, W and Gan, W and Zhang, T}, title = {Chlamydia psittaci pneumonia: a clinical analysis of 12 patients.}, journal = {Annals of translational medicine}, volume = {11}, number = {3}, pages = {144}, pmid = {36846017}, issn = {2305-5839}, abstract = {BACKGROUND: We conducted a retrospective analysis to explore the clinical characteristics, laboratory examination, imaging features, treatment outcomes, and prognosis of the Chlamydia psittaci (C. psittaci) pneumonia, aiming to improve early diagnosis and treatment.<br><br>METHODS: The clinical data of 12 patients with C. psittaci pneumonia diagnosed by metagenomic next-generation sequencing (mNGS) in our hospital were retrospectively analyzed. These data included baseline information, epidemiological history, clinical symptoms and signs, laboratory and chest computed tomography (CT) examination findings, treatment schemes, and prognosis.<br><br>RESULTS: The average age of the 12 patients was 58.25&#xb1;13.27 years, and there were 7 (58.3%) males and 5 (41.7%) females in this cohort. Five patients had clear exposure to poultry or birds. The main clinical manifestations included fever (12/12, 100.0%), cough (12/12, 100.0%), expectoration (10/12, 83.3%), and dyspnea (10/12, 83.3%). Laboratory examination showed marked elevation of the total white blood cell (WBC) count, neutrophil (NEUT) count, C-reactive protein (CRP), procalcitonin (PCT), D-dimer, aspartate aminotransferase (AST), alanine aminotransferase (ALT), serum creatinine, and creatine kinase (CK) levels; as well as decreased hemoglobin (HGB), blood platelet (PLT), and albumin (ALB) levels. Arterial blood gas analysis showed that the average value of the oxygenation index (PO2/FiO2) was 290.9&#xb1;83.1, which was less than 300 in 6 cases (50.0%). The main chest CT features were patchy or consolidation in the bilateral or unilateral lungs, and the boundary was not clear but showed a bronchial inflation sign. Also, some of the cases were accompanied by pleural effusion. Once the etiology was obtained, the patients were quickly treated with doxycycline combined with other antibiotics. All 12 patients improved and were discharged from the hospital. However, two severe patients were admitted to the intensive care unit (ICU) and received ventilation and monitoring treatment. There were no deaths.<br><br>CONCLUSIONS: C. psittaci pneumonia is an atypical community-acquired pneumonia (CAP) caused by C. psittaci infection, with its own laboratory and imaging characteristics. In this study, diagnosis was established based on the application of mNGS owing to the absence of easily available conventional pathogenic evidence. In addition, an aggressive and precise treatment strategy can help achieve a favorable prognosis for patients.}, }
@article {pmid36844847, year = {2023}, author = {Shi, Y and Guo, W and Hu, M and Wang, Y and Li, J and Hu, W and Li, X and Xu, K}, title = {A case of severe leptospirosis with Jarisch-Herxheimer reaction presenting as respiratory failure.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1125306}, pmid = {36844847}, issn = {2296-2565}, abstract = {BACKGROUND: Leptospirosis is a widespread zoonotic disease caused by pathogenic Leptospira spp. The treatment of penicillin or tetracycline can cause a Jarisch-Herxheimer reaction (JHR), which can lead to acute respiratory distress syndrome (ARDS) and multi-organ failure in severe cases. The overall course of evolution and imaging features of a JHR exacerbation of leptospirosis have rarely been reported.<br><br>CASE PRESENTATION: We present a case of leptospirosis complicated by pulmonary alveolar hemorrhage and a Jarisch-Herxheimer reaction (JHR) that required respiratory and vasopressor support. This case demonstrates a well-defined course of evolution of JHR and the imaging features.<br><br>CONCLUSIONS: Leptospirosis is easily misdiagnosed in some sporadic areas, and JHR complicates its management. Early diagnosis and appropriate treatment can reduce the mortality of severe leptospirosis with JHR.}, }
@article {pmid36844675, year = {2023}, author = {Dai, Q and Ding, J and Cui, X and Zhu, Y and Chen, H and Zhu, L}, title = {Beyond bacteria: Reconstructing microorganism connections and deciphering the predicted mutualisms in mammalian gut metagenomes.}, journal = {Ecology and evolution}, volume = {13}, number = {2}, pages = {e9829}, pmid = {36844675}, issn = {2045-7758}, abstract = {Numerous gut microbial studies have focused on bacteria. However, archaea, viruses, fungi, protists, and nematodes are also regular residents of the gut ecosystem. Little is known about the composition and potential interactions among these six kingdoms in the same samples. Here, we unraveled the complex connection among them using approximately 123 gut metagenomes from 42 mammalian species (including carnivores, omnivores, and herbivores). We observed high variation in bacterial and fungal families and relatively low variation in archaea, viruses, protists, and nematodes. We found that some fungi in the mammalian intestine might come from environmental sources (e.g., soil and dietary plants), and some might be native to the intestine (e.g., the occurrence of Neocallimastigomycetes). The Methanobacteriaceae and Plasmodiidae families (archaea and protozoa, respectively) were predominant in these metagenomes, whereas Onchocercidae and Trichuridae were the two most common nematodes, and Siphoviridae and Myoviridae the two most common virus families in these mammalian gut metagenomes. Interestingly, most of the pairwise co-occurrence patterns were significantly positive among these six kingdoms, and significantly negative networks mainly occurred between fungi and prokaryotes (both bacteria and archaea). Our study revealed some inconvenient characteristics in the mammalian gut microorganism ecosystem: (1) the community formed by members of the analyzed kingdoms reflects the life history of the host and the potential threat posed by pathogenic protists and nematodes in mammals; and (2) the networks suggest the existence of predicted mutualism among members of these six kingdoms and of the predicted competition, mainly among fungi and other kingdoms.}, }
@article {pmid36844641, year = {2023}, author = {Tashkandi, M and Baz, L}, title = {Function of CAZymes encoded by highly abundant genes in rhizosphere microbiome of Moringa oleifera.}, journal = {Saudi journal of biological sciences}, volume = {30}, number = {3}, pages = {103578}, pmid = {36844641}, issn = {1319-562X}, abstract = {Metagenomic analysis referring to CAZymes (Carbohydrate-Active enZymes) of CAZy classes encoded by the most abundant genes in rhizosphere versus bulk soil microbes of the wild plant Moringa oleifera was conducted. Results indicated that microbiome signatures and corresponding CAZy datasets differ between the two soil types. CAZy class glycoside hydrolases (GH) and its α-amylase family GH13 in rhizobiome were proven to be the most abundant among CAZy classes and families. The most abundant bacteria harboring these CAZymes include phylum Actinobacteria and its genus Streptomyces and phylum Proteobacteria and its genus Microvirga. These CAZymes participate in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway "Starch and sucrose metabolism" and mainly use the "double displacement catalytic mechanism" in their reactions. We assume that microbiome of the wild plant Moringa oleifera is a good source of industrially important enzymes that act on starch hydrolysis and/or biosynthesis. In addition, metabolic engineering and integration of certain microbes of this microbiomes can also be used in improving growth of domestic plants and their ability to tolerate adverse environmental conditions.}, }
@article {pmid36844406, year = {2023}, author = {Stout, MJ and Brar, AK and Herter, BN and Rankin, A and Wylie, KM}, title = {The plasma virome in longitudinal samples from pregnant patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1061230}, pmid = {36844406}, issn = {2235-2988}, abstract = {INTRODUCTION: Nucleic acid from viruses is common in peripheral blood, even in asymptomatic individuals. How physiologic changes of pregnancy impact host-virus dynamics for acute, chronic, and latent viral infections is not well described. Previously we found higher viral diversity in the vagina during pregnancy associated with preterm birth (PTB) and Black race. We hypothesized that higher diversity and viral copy numbers in the plasma would show similar trends.<br><br>METHODS: To test this hypothesis, we evaluated longitudinally collected plasma samples from 23 pregnant patients (11 term and 12 preterm) using metagenomic sequencing with ViroCap enrichment to enhance virus detection. Sequence data were analyzed with the ViroMatch pipeline.<br><br>RESULTS: We detected nucleic acid from at least 1 virus in at least 1 sample from 87% (20/23) of the maternal subjects. The viruses represented 5 families: Herpesviridae, Poxviridae, Papillomaviridae, Anelloviridae, and Flaviviridae. We analyzed cord plasma from 18 of the babies from those patients and found nucleic acid from viruses in 33% of the samples (6/18) from 3 families: Herpesviridae, Papillomaviridae, and Anelloviridae. Some viral genomes were found in both maternal plasma and cord plasma from maternal-fetal pairs (e.g. cytomegalovirus, anellovirus). We found that Black race associated with higher viral richness (number of different viruses detected) in the maternal blood samples (P=0.003), consistent with our previous observations in vaginal samples. We did not detect associations between viral richness and PTB or the trimester of sampling. We then examined anelloviruses, a group of viruses that is ubiquitous and whose viral copy numbers fluctuate with immunological state. We tested anellovirus copy numbers in plasma from 63 pregnant patients sampled longitudinally using qPCR. Black race associated with higher anellovirus positivity (P<0.001) but not copy numbers (P=0.1). Anellovirus positivity and copy numbers were higher in the PTB group compared to the term group (P<0.01, P=0.003, respectively). Interestingly, these features did not occur at the time of delivery but appeared earlier in pregnancy, suggesting that although anelloviruses were biomarkers for PTB they were not triggering parturition.<br><br>DISCUSSION: These results emphasize the importance of longitudinal sampling and diverse cohorts in studies of virome dynamics during pregnancy.}, }
@article {pmid36844401, year = {2023}, author = {Zhang, G and Zhang, H and Hu, X and Xu, D and Tang, B and Tang, M and Liu, S and Li, Y and Xu, W and Guo, C and Gao, Q}, title = {Clinical application value of metagenomic next-generation sequencing in the diagnosis of spinal infections and its impact on clinical outcomes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1076525}, pmid = {36844401}, issn = {2235-2988}, abstract = {This study aimed to evaluate the impact of precise treatment administered according to the results of metagenomic next-generation sequencing (mNGS) on the clinical outcomes of patients with spinal infections. In this multicenter retrospective study, the clinical data of 158 patients with spinal infections who were admitted to Xiangya Hospital Central South University, Xiangya Boai Rehabilitation Hospital, The First Hospital of Changsha, and Hunan Chest Hospital from 2017 to 2022 were reviewed. Among these 158 patients, 80 patients were treated with targeted antibiotics according to the mNGS results and were assigned to the targeted medicine (TM) group. The remaining 78 patients with negative mNGS results and those without mNGS and negative microbial culture results were treated with empirical antibiotics and assigned to the empirical drug (EM) group. The impact of targeted antibiotics based on the mNGS results on the clinical outcomes of patients with spinal infections in the two groups was analyzed. The positive rate of mNGS for diagnosing spinal infections was significantly higher than that of microbiological culture (X [2]=83.92, P<0.001), procalcitonin (X [2]=44.34, P<0.001), white blood cells (X [2]=89.21, P < 0.001), and IGRAs (Interferon-gamma Release Tests) (X [2] = 41.50, P < 0.001). After surgery, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) showed a decreasing trend in the patients with spinal infections in both the TM and EM groups. The decrease in CRP was more obvious in the TM group than in the EM group at 7, 14 days, 3, and 6 months after surgery (P<0.05). The decrease in ESR was also significantly obvious in the TM group compared with the EM group at 1 and 6 months after surgery (P<0.05). The time taken for CRP and ESR to return to normal in the TM group was significantly shorter than that in the EM group (P<0.05). There was no significant difference in the incidence of poor postoperative outcomes between the two groups. The positive rate of mNGS for the diagnosis of spinal infection is significantly higher than that of traditional detection methods. The use of targeted antibiotics based on mNGS results could enable patients with spinal infections to achieve a faster clinical cure.}, }
@article {pmid36844396, year = {2023}, author = {Qin, C and Zhang, S and Zhao, Y and Ding, X and Yang, F and Zhao, Y}, title = {Diagnostic value of metagenomic next-generation sequencing in sepsis and bloodstream infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1117987}, pmid = {36844396}, issn = {2235-2988}, abstract = {OBJECTIVE: To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in sepsis and bloodstream infection (BSI).<br><br>METHODS: A retrospective analysis of patients diagnosed with sepsis and BSI at the First Affiliated Hospital of Zhengzhou University from January 2020 to February 2022 was conducted. All the patients underwent blood culture and were divided into mNGS group and non-mNGS group according to whether mNGS was performed or not. The mNGS group was further divided into early group (< 1 day), intermediate group (1-3 days), and late group (> 3 days) according to the time of mNGS inspection.<br><br>RESULTS: In 194 patients with sepsis and BSI, the positive rate of mNGS for identifying pathogens was significantly higher than that of blood culture (77.7% vs. 47.9%), and the detection period was shorter (1.41 &#xb1; 1.01 days vs. 4.82 &#xb1; 0.73 days); the difference was statistically significant (p < 0.05). The 28-day mortality rate of the mNGS group (n = 112) was significantly lower than that of the non-mNGS group (n = 82) (47.32% vs. 62.20%, p = 0.043). The total hospitalization time for the mNGS group was longer than that for the non-mNGS group (18 (9, 33) days vs. 13 (6, 23) days, p = 0.005). There was no significant difference in the ICU hospitalization time, mechanical ventilation time, vasoactive drug use time, and 90-day mortality between the two groups (p > 0.05). Sub-group analysis of patients in the mNGS group showed that the total hospitalization time and the ICU hospitalization time in the late group were longer than those in the early group (30 (18, 43) days vs. 10 (6, 26) days, 17 (6, 31) days vs. 6 (2, 10) days), and the ICU hospitalization time in the intermediate group was longer than that in the early group (6 (3, 15) days vs. 6 (2, 10) days); the differences were statistically significant (p&#xa0;< 0.05). The 28-day mortality rate of the early group was higher than that of the late group (70.21% vs. 30.00%), and the difference was statistically significant (p = 0.001).<br><br>CONCLUSIONS: mNGS has the advantages of a short detection period and a high positive rate in the diagnosis of pathogens causing BSI and, eventually, sepsis. Routine blood culture combined with mNGS can significantly reduce the mortality of septic patients with BSI. Early detection using mNGS can shorten the total hospitalization time and the ICU hospitalization time of patients with sepsis and BSI.}, }
@article {pmid36844226, year = {2023}, author = {Liu, Y and Mo, X and Feng, Y and Willoughby, RE and Weng, X and Wang, Y and Li, X and Gao, J and Tian, J and Peng, J}, title = {Metagenomic next-generation sequencing for the etiological diagnosis of rabies virus in cerebrospinal fluid.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {982290}, pmid = {36844226}, issn = {2296-858X}, abstract = {BACKGROUND: Rabies is a highly fatal disease. Once symptoms develop, death usually occurs within days. Survivors were occasionally reported in the literatures. Ante-mortem diagnosis remains a challenge in most rabies endemic countries. A novel, accurate diagnostic assay is highly desirable.<br><br>METHODS: We used metagenomic next-generation sequencing (mNGS) to examine the cerebrospinal fluid (CSF) samples of a 49-year-old patient with rabies and validated the results by TaqMan PCR and RT-PCR/Sanger sequencing.<br><br>RESULTS: Metagenomic next-generation sequencing identified sequence reads uniquely aligned to the rabies virus (RABV). PCR confirmed the presence of the partial RABV N gene in the CSF. Phylogenetic analysis showed that the RABV grouped as an Asian clade, which is the most broadly distributed clade in China.<br><br>CONCLUSION: Metagenomic next-generation sequencing may be a useful screening tool for the etiological diagnosis of rabies, especially in the absence of timely rabies laboratory testing or in patients with no exposure history.}, }
@article {pmid36843502, year = {2023}, author = {Winder, JC and Braga, LPP and Kuhn, MA and Thompson, LM and Olefeldt, D and Tanentzap, AJ}, title = {Climate warming has direct and indirect effects on microbes associated with carbon cycling in northern lakes.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.16655}, pmid = {36843502}, issn = {1365-2486}, abstract = {Northern lakes disproportionately influence the global carbon cycle, and may do so more in the future depending on how their microbial communities respond to climate warming. Microbial communities can change because of the direct effects of climate warming on their metabolism and the indirect effects of climate warming on groundwater connectivity from thawing of surrounding permafrost, especially at lower landscape positions. Here we used shotgun metagenomics to compare the taxonomic and functional gene composition of sediment microbes in 19 peatland lakes across a 1600-km permafrost transect in boreal western Canada. We found microbes responded differently to the loss of regional permafrost cover than to increases in local groundwater connectivity. These results suggest that both the direct and indirect effects of climate warming, which were respectively associated with loss of permafrost thaw and subsequent changes in groundwater connectivity interact to change microbial composition and function. Archaeal methanogens and genes involved in all major methanogenesis pathways were more abundant in warmer regions with less permafrost, but higher groundwater connectivity partly offset these effects. Bacterial community composition and methanotrophy genes did not vary with regional permafrost cover, and the latter changed similarly to methanogenesis with groundwater connectivity. Finally, we found an increase in sugar utilisation genes in regions with less permafrost, which may further fuel methanogenesis. These results provide the microbial mechanism for observed increases in methane emissions associated with loss of permafrost cover in this region and suggest that future emissions will primarily be controlled by archaeal methanogens over methanotrophic bacteria as northern lakes warm. Our study more generally suggests that future predictions of aquatic carbon cycling will be improved by considering how climate warming exerts both direct effects associated with regional-scale permafrost thaw and indirect effects associated with local hydrology.}, }
@article {pmid36843227, year = {2023}, author = {Lynch, LE and Hair, AB and Soni, KG and Yang, H and Gollins, LA and Narvaez-Rivas, M and Setchell, KDR and Preidis, GA}, title = {Cholestasis impairs gut microbiota development and bile salt hydrolase activity in preterm neonates.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2183690}, doi = {10.1080/19490976.2023.2183690}, pmid = {36843227}, issn = {1949-0984}, abstract = {Cholestasis refers to impaired bile flow from the liver to the intestine. In neonates, cholestasis causes poor growth and may progress to liver failure and death. Normal bile flow requires an intact liver-gut-microbiome axis, whereby liver-derived primary bile acids are transformed into secondary bile acids. Microbial bile salt hydrolase (BSH) enzymes are responsible for the first step, deconjugating glycine- and taurine-conjugated primary bile acids. Cholestatic neonates often are treated with the potent choleretic bile acid ursodeoxycholic acid (UDCA), although interactions between UDCA, gut microbes, and other bile acids are poorly understood. To gain insight into how the liver-gut-microbiome axis develops in extreme prematurity and how cholestasis alters this maturation, we conducted a nested case-control study collecting 124 stool samples longitudinally from 24 preterm infants born at mean 27.2 ± 1.8 weeks gestation and 946 ± 249.6 g, half of whom developed physiologic cholestasis. Samples were analyzed by whole metagenomic sequencing, in vitro BSH enzyme activity assays optimized for low biomass fecal samples, and quantitative mass spectrometry to measure the bile acid metabolome. In extremely preterm neonates, acquisition of the secondary bile acid biosynthesis pathway and BSH genes carried by Clostridium perfringens are the most prominent features of early microbiome development. Cholestasis interrupts this developmental pattern. BSH gene abundance and enzyme activity are profoundly reduced in cholestatic neonates, resulting in decreased quantities of unconjugated bile acids. UDCA restores total fecal bile acid levels in cholestatic neonates, but this is due to a 522-fold increase in fecal UDCA. A majority of bile acids in early development are atypical positional and stereo-isomers of bile acids. We report novel associations linking isomeric bile acids and BSH activity to neonatal growth trajectories. These data highlight deconjugation of bile acids as a key microbial function that is acquired in early neonatal development and impaired by cholestasis.}, }
@article {pmid36842848, year = {2023}, author = {Ojala, T and Kankuri, E and Kankainen, M}, title = {Understanding human health through metatranscriptomics.}, journal = {Trends in molecular medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molmed.2023.02.002}, pmid = {36842848}, issn = {1471-499X}, abstract = {Metatranscriptomics has revolutionized our ability to explore and understand transcriptional programs in microbial communities. Moreover, it has enabled us to gain deeper and more specific insight into the microbial activities in human gut, respiratory, oral, and vaginal communities. Perhaps the most important contribution of metatranscriptomics arises, however, from the analyses of disease-associated communities. We review the advantages and disadvantages of metatranscriptomics analyses in understanding human health and disease. We focus on human tissues low in microbial biomass and conditions associated with dysbiotic microbiota. We conclude that a more widespread use of metatranscriptomics and increased knowledge on microbe activities will uncover critical interactions between microbes and host in human health and provide diagnostic basis for culturing-independent, direct functional pathogen identification.}, }
@article {pmid36842577, year = {2023}, author = {Wang, F and Zhang, L and Luo, Y and Li, Y and Cheng, X and Cao, J and Wu, J and Huang, H and Luo, J and Su, Y}, title = {Surfactant aggravated the antibiotic's stress on antibiotic resistance genes proliferation by altering antibiotic solubilization and microbial traits in sludge anaerobic fermentation.}, journal = {The Science of the total environment}, volume = {873}, number = {}, pages = {162440}, doi = {10.1016/j.scitotenv.2023.162440}, pmid = {36842577}, issn = {1879-1026}, abstract = {The excessive application of antibiotics and surfactants resulted in their massive accumulation in waste activated sludge (WAS), but the co-occurrent impacts of antibiotics and surfactants on the antibiotic resistant genes (ARGs) fates have seldom reported. This work mainly revealed the roles and critical mechanisms of sodium dodecyl benzene sulfonate (SDBS) on the sulfadiazine (SDZ) stressing for ARGs distribution during WAS anaerobic fermentation. High-throughput qPCR and metagenomic analysis revealed that SDBS aggravated the SDZ selective pressure, and accelerated the proliferation of ARGs. The total abundance of ARGs was increased from 8.81 × 10[10] in SDZ to 1.17 × 10[11] copies/g TSS in the SDBS/SDZ co-occurrence system. Specifically, the absolute abundances of ermF (MLSB), mefA (MLSB), tetM-01 (tetracycline), tetX (tetracycline), sul2 (sulfonamide) and strB (aminoglycoside) were risen from 4.60 × 10[8]-7.44 × 10[9] copies/g TSS in the SDZ reactor to 1.02 × 10[9]-4.63 × 10[10] copies/g TSS in SDBS/SDZ reactor. SDBS was contributed to the SDZ solubilization and simultaneously effective in disintegrating extracellular polymeric substances and improving cell membrane permeability, which would facilitate the SDZ transport and its interactions with ARGs hosts. Consequently, the microbial community structure was evidently altered, and the typical ARGs hosts (i.e., Saccharimonadales and Ahniella) were greatly enriched. Also, the cell signal transduction systems (i.e., glnL, glrK and pilG), oxidative stress response (i.e., frmA and recA) and bacterial secretion systems (i.e., VirB4), which were related with ARGs propagation, were all provoked in the co-occurred SDBS/SDZ reactor compared with that of sole SDZ. PLS-PM analysis suggested that the bacterial community was the predominant factor that determined the ARGs fates, followed by mobile genetic elements and metabolic pathway. This work demonstrated the interactive effects of surfactants and antibiotics on the ARGs fates in WAS fermentation systems and gave insightful implications on the ecological risks of different exogenous pollutants.}, }
@article {pmid36842329, year = {2023}, author = {Zhou, L and Zhao, B and Zhuang, WQ}, title = {Double-edged sword effects of dissimilatory nitrate reduction to ammonium (DNRA) bacteria on anammox bacteria performance in an MBR reactor.}, journal = {Water research}, volume = {233}, number = {}, pages = {119754}, doi = {10.1016/j.watres.2023.119754}, pmid = {36842329}, issn = {1879-2448}, abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) bacteria imposing double-edged sword effects on anammox bacteria were investigated in an anammox-membrane bioreactor (MBR) experiencing an induced crash-recovery event. During the experiment, the anammox-MBR was loaded with NH4[+]-N:NO2[-]-N ratios (RatioNH4[+]-N: NO2[-]-N) of 1.20-1.60. Initially, the anammox-MBR removed over 95% of 100 mg/L NH4[+]-N and 132 mg/L NO2[-]-N (RatioNH4[+]-N: NO2[-]-N = 0.76, the well accepted stoichiometric RatioNH4[+]-N: NO2[-]-N for anammox) in the influent (Stage 0). Then, we induced a system crash-recovery event via nitrite shock loadings to better understand responses from different guilds of bacteria in anammox-MBR, loaded with 1.60 RatioNH4[+]-N: NO2[-]-N with 100 mg/L NO2[-]-N in the influent (Stage 1). Interestingly, the nitrogen removal by anammox bacteria was maintained for about 20 days before starting to decrease significantly. In Stage 2, we further increased influent nitrite concentration to 120 mg/L (1.33 RatioNH4[+]-N: NO2[-]-N) to simulate a high nitrite toxicity scenario for a short period of time. As expected, nitrogen removal efficiency dropped to only 16.8%. After the induced system crash, anammox-MBR performance recovered steadily to 93.2% nitrogen removal with a 1.25 RatioNH4[+]-N:NO2[-]-N and a low nitrite influent concentration of 80 mg/L NO2[-]-N. Metagenomics analysis revealed that a probable causality of the decreasing nitrogen removal efficiency in Stage 1 was the overgrowth of DNRA-capable bacteria. The results showed that the members within the Ignavibacteriales order (21.7%) out competed anammox bacteria (17.0%) in the anammox-MBR with elevated nitrite concentrations in the effluent. High NO2[-]-N loading (120 mg N/L) further caused the predominant Candidatus Kuenenia spp. were replaced by Candidatus Brocadia spp. Therefore, it was evident that DNRA bacteria posed negative effects on anammox with 1.60 RatioNH4[+]-N: NO2[-]-N. Also, when 120 mg/L NO2[-]-N fed to anammox-MBR (RatioNH4[+]-N: NO2[-]-N = 1.33), canonical denitrification became the primary nitrogen sink with both DNRA and anammox activities decreased. They probably fed on lysed microbial cells of anammox and DNRA. In Stage 3, a low RatioNH4[+]-N: NO2[-]-N (1.25) with 80 mg/L NO2[-]-N was used to rescue the system, which effectively promoted DNRA-capable bacteria growth. Although anammox bacteria's abundance was only 7.7% during this stage, they could be responsible for about 90% of the total nitrogen removal during this stage.}, }
@article {pmid36841901, year = {2023}, author = {Doré, H and Guyet, U and Leconte, J and Farrant, GK and Alric, B and Ratin, M and Ostrowski, M and Ferrieux, M and Brillet-Guéguen, L and Hoebeke, M and Siltanen, J and Le Corguillé, G and Corre, E and Wincker, P and Scanlan, DJ and Eveillard, D and Partensky, F and Garczarek, L}, title = {Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {36841901}, issn = {1751-7370}, abstract = {The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, especially for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we show that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We also identify clusters of adjacent genes that display specific distribution patterns in the field (eCAGs) and are thus potentially involved in the same metabolic pathway and may have a key role in niche adaptation. Several eCAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine, or phosphonates, which might be either directly used by cells, for example for the biosynthesis of proteins or DNA, or degraded to inorganic nitrogen and/or phosphorus forms. We also highlight the enrichment of eCAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas vs. low-iron (Fe) regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in the latter areas. In contrast, Prochlorococcus populations thriving in Fe-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) to Fe(II). Altogether, this study provides insights into how phytoplankton communities populate oceanic ecosystems, which is relevant to understanding their capacity to respond to ongoing climate change.}, }
@article {pmid36840602, year = {2023}, author = {Schildkraut, JA and Coolen, JPM and Severin, H and Koenraad, E and Aalders, N and Melchers, WJG and Hoefsloot, W and Wertheim, HFL and van Ingen, J}, title = {MGIT Enriched Shotgun Metagenomics for Routine Identification of Nontuberculous Mycobacteria: a Route to Personalized Health Care.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0131822}, doi = {10.1128/jcm.01318-22}, pmid = {36840602}, issn = {1098-660X}, abstract = {Currently, nontuberculous mycobacteria (NTM) are identified using small genomic regions, and species-level identification is often not possible. We introduce a next-generation sequencing (NGS) workflow that identifies mycobacteria to (sub)species level on the basis of the whole genome extracted from enriched shotgun metagenomic data. This technique is used to study the association between genotypes and clinical manifestations to pave the way to more personalized health care. Two sets of clinical isolates (explorative set [n = 212] and validation set [n = 235]) were included. All data were analyzed using a custom pipeline called MyCodentifier. Sequences were matched against a custom hsp65 database (NGS-hsp65) and whole-genome database (NGS-WG) created based on the phylogeny presented by Tortoli et al. (E. Tortoli, T. Fedrizzi, C. J. Meehan, A. Trovato, et al., Infect Genet Evol 56:19-25, 2017, https://doi.org/10.1016/j.meegid.2017.10.013). Lastly, phylogenetic analysis was performed and correlated with clinical manifestation. In the explorative set, we observed 98.6% agreement between the line probe assay and the NGS-hsp65 database. In the validation set, 99.1% agreement between the NGS-WG and NGS-hsp65 databases was seen on the complex level. We identified a cluster of Mycobacterium marinum isolates not represented by the Tortoli et al. phylogeny. Phylogenetic analysis of M. avium complex isolates confirmed misclassification of M. timonense and M. bouchedurhonense and identified subclusters within M. avium although no correlation with clinical manifestation was observed. We performed routine NGS to identify NTM from MGIT enriched shotgun metagenomic data. Phylogenetic analyses identified subtypes of M. avium, but in our set of isolates no correlation with clinical manifestation was found. However, this NGS workflow paves a way for more personalized health care in the future.}, }
@article {pmid36840579, year = {2023}, author = {Rix, GD and Sims, LP and Dawson, RA and Williamson, G and Bryant, Y and Crombie, AT and Murrell, JC}, title = {Analysis of Essential Isoprene Metabolic Pathway Proteins in Variovorax sp. Strain WS11.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0212222}, doi = {10.1128/aem.02122-22}, pmid = {36840579}, issn = {1098-5336}, abstract = {Isoprene monooxygenase (IsoMO, encoded by isoABCDEF) initiates the oxidation of the climate-active gas isoprene, with the genes isoGHIJ and aldH nearly always found adjacent to isoABCDEF in extant and metagenome-derived isoprene degraders. The roles of isoGHIJ and aldH are uncertain, although each is essential to isoprene degradation. We report here the characterization of these proteins from two model isoprene degraders, Rhodococcus sp. strain AD45 and Variovorax sp. strain WS11. The genes isoHIJ and aldH from Variovorax and aldH from Rhodococcus were expressed individually in Escherichia coli as maltose binding protein fusions to overcome issues of insolubility. The activity of two glutathione S-transferases from Variovorax, IsoI and IsoJ was assessed with model substrates, and the conversion of epoxyisoprene to the intermediate 1-hydroxy-2-glutathionyl-2-methyl-3-butene (HGMB) was demonstrated. The next step of the isoprene metabolic pathway of Variovorax is catalyzed by the dehydrogenase IsoH, resulting in the conversion of HGMB to 2-glutathionyl-2-methyl-3-butenoic acid (GMBA). The aldehyde dehydrogenases (AldH) from Variovorax and Rhodococcus were examined with a variety of aldehydes, with both exhibiting maximum activity with butanal. AldH significantly increased the rate of production of NADH when added to the IsoH-catalyzed conversion of HGMB to GMBA (via GMB), suggesting a synergistic role for AldH in the isoprene metabolic pathway. An in silico analysis of IsoG revealed that this protein, which is essential for isoprene metabolism in Variovorax, is an enzyme of the formyl CoA-transferase family and is predicted to catalyze the formation of a GMBA-CoA thioester as an intermediate in the isoprene oxidation pathway. IMPORTANCE Isoprene is a climate-active gas, largely produced by trees, which is released from the biosphere in amounts equivalent to those of methane and all other volatile organic compounds combined. Bacteria found in many environments, including soils and on the surface of leaves of isoprene-producing trees, can grow on isoprene and thus may represent a significant biological sink for this globally significant volatile compound and remove isoprene before it escapes to the atmosphere, thus reducing its potency as a climate-active gas. The initial oxidation of isoprene by bacteria is mediated by isoprene monooxygenase encoded by the genes isoABCDEF. In isoprene-degrading bacteria, a second gene cluster, isoGHIJ, is also present, although the exact role in isoprene degradation by the proteins encoded by these genes is uncertain. This investigation sheds new light on the roles of these proteins in the isoprene oxidation pathway in two model isoprene-degrading bacteria of the genera Rhodococcus and Variovorax.}, }
@article {pmid36840260, year = {2023}, author = {Anguita-Maeso, M and Navas-Cortés, JA and Landa, BB}, title = {Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, doi = {10.3390/plants12040912}, pmid = {36840260}, issn = {2223-7747}, abstract = {Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.}, }
@article {pmid36840091, year = {2023}, author = {Kutasy, B and Kiniczky, M and Decsi, K and Kálmán, N and Hegedűs, G and Alföldi, ZP and Virág, E}, title = {'Garlic-lipo'4Plants: Liposome-Encapsulated Garlic Extract Stimulates ABA Pathway and PR Genes in Wheat (Triticum aestivum).}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, doi = {10.3390/plants12040743}, pmid = {36840091}, issn = {2223-7747}, abstract = {Recently, environmentally friendly crop improvements using next-generation plant biostimulants (PBs) come to the forefront in agriculture, regardless of whether they are used by scientists, farmers, or industries. Various organic and inorganic solutions have been investigated by researchers and producers, focusing on tolerance to abiotic and biotic stresses, crop quality, or nutritional deficiency. Garlic has been considered a universal remedy ever since antiquity. A supercritical carbon dioxide garlic extract encapsulated in nanoscale liposomes composed of plant-derived lipids was examined as a possible PB agent. The present study focused on the characterization of the genes associated with the pathways involved in defense response triggered by the liposome nanoparticles that were loaded with supercritical garlic extracts. This material was applied to Triticum aestivum in greenhouse experiments using foliar spraying. The effects were examined in a large-scale genome-wide transcriptional profiling experiment by collecting the samples four times (0 min, used as a control, and 15 min, 24 h, and 48 h after spraying). Based on a time-course expression analysis, the dynamics of the cellular response were determined by examining differentially expressed genes and applying a cluster analysis. The results suggested an enhanced expression of abscisic acid (ABA) pathway and pathogenesis-related (PR) genes, of which positive regulation was found for the AP2-, C2H2-, HD-ZIP-, and MYB-related transcription factor families.}, }
@article {pmid36839335, year = {2023}, author = {Ezzatpour, S and Mondragon Portocarrero, ADC and Cardelle-Cobas, A and Lamas, A and López-Santamarina, A and Miranda, JM and Aguilar, HC}, title = {The Human Gut Virome and Its Relationship with Nontransmissible Chronic Diseases.}, journal = {Nutrients}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/nu15040977}, pmid = {36839335}, issn = {2072-6643}, abstract = {The human gastrointestinal tract contains large communities of microorganisms that are in constant interaction with the host, playing an essential role in the regulation of several metabolic processes. Among the gut microbial communities, the gut bacteriome has been most widely studied in recent decades. However, in recent years, there has been increasing interest in studying the influences that other microbial groups can exert on the host. Among them, the gut virome is attracting great interest because viruses can interact with the host immune system and metabolic functions; this is also the case for phages, which interact with the bacterial microbiota. The antecedents of virome-rectification-based therapies among various diseases were also investigated. In the near future, stool metagenomic investigation should include the identification of bacteria and phages, as well as their correlation networks, to better understand gut microbiota activity in metabolic disease progression.}, }
@article {pmid36839325, year = {2023}, author = {Halimulati, M and Wang, R and Aihemaitijiang, S and Huang, X and Ye, C and Zhang, Z and Li, L and Zhu, W and Zhang, Z and He, L}, title = {Anti-Hyperuricemic Effect of Anserine Based on the Gut-Kidney Axis: Integrated Analysis of Metagenomics and Metabolomics.}, journal = {Nutrients}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/nu15040969}, pmid = {36839325}, issn = {2072-6643}, abstract = {Nowadays, developing effective intervention substances for hyperuricemia has become a public health issue. Herein, the therapeutic ability of anserine, a bioactive peptide, was validated through a comprehensive multiomics analysis of a rat model of hyperuricemia. Anserine was observed to improve liver and kidney function and modulate urate-related transporter expressions in the kidneys. Urine metabolomics showed that 15 and 9 metabolites were significantly increased and decreased, respectively, in hyperuricemic rats after the anserine intervention. Key metabolites such as fructose, xylose, methionine, erythronic acid, glucaric acid, pipecolic acid and trans-ferulic acid were associated with ameliorating kidney injury. Additionally, anserine regularly changed the gut microbiota, thereby ameliorating purine metabolism abnormalities and alleviating inflammatory responses. The integrated multiomics analysis indicated that Saccharomyces, Parasutterella excrementihominis and Emergencia timonensis were strongly associated with key differential metabolites. Therefore, we propose that anserine improved hyperuricemia via the gut-kidney axis, highlighting its potential in preventing and treating hyperuricemia.}, }
@article {pmid36839205, year = {2023}, author = {Ye, W and Chen, Z and He, Z and Gong, H and Zhang, J and Sun, J and Yuan, S and Deng, J and Liu, Y and Zeng, A}, title = {Lactobacillus plantarum-Derived Postbiotics Ameliorate Acute Alcohol-Induced Liver Injury by Protecting Cells from Oxidative Damage, Improving Lipid Metabolism, and Regulating Intestinal Microbiota.}, journal = {Nutrients}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/nu15040845}, pmid = {36839205}, issn = {2072-6643}, abstract = {Here, the aim was to evaluate the protective effect of Lactobacillus plantarum-derived postbiotics, i.e., LP-cs, on acute alcoholic liver injury (ALI). After preincubation with LP-cs, HL7702 human hepatocytes were treated with alcohol, and then the cell survival rate was measured. C57BL/6 male mice were presupplemented with or without LP-cs and LP-cs-loaded calcium alginate hydrogel (LP-cs-Gel) for 3 weeks and given 50% alcohol gavage to establish the mouse model of ALI, LP-cs presupplementation, and LP-cs-Gel presupplementation. The histomorphology of the liver and intestines; the levels of serum AST, ALT, lipid, and SOD activity; liver transcriptomics; and the metagenome of intestinal microbiota were detected in all mouse models. In vitro, LP-cs significantly increased the survival rate of alcohol-treated cells. In vivo, presupplementation with LP-cs and LP-cs-Gel restored the levels of serum AST, ALT, and SOD activity, as well as TC and TG, after acute alcohol intake. In the LP-cs-presupplemented mice, the genes involved in fatty acid metabolic processes were upregulated and the genes involved in steroid biosynthesis were downregulated significantly as compared with the ALI mice. LP-cs significantly increased the abundance of intestinal microbiota, especially Akkermansia muciniphila. In conclusion, LP-cs ameliorates ALI by protecting hepatocytes against oxidative damage, thereby, improving lipid metabolism and regulating the intestinal microbiota. The effect of LP-cs-Gel is similar to that of LP-cs.}, }
@article {pmid36838868, year = {2023}, author = {Shao, Y and Wang, W and Hu, Y and Gänzle, MG}, title = {Characterization of the Glucan-Branching Enzyme GlgB Gene from Swine Intestinal Bacteria.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {4}, pages = {}, doi = {10.3390/molecules28041881}, pmid = {36838868}, issn = {1420-3049}, abstract = {Starch hydrolysis by gut microbiota involves a diverse range of different enzymatic activities. Glucan-branching enzyme GlgB was identified as the most abundant glycosidase in Firmicutes in the swine intestine. GlgB converts α-(1→4)-linked amylose to form α-(1→4,6) branching points. This study aimed to characterize GlgB cloned from a swine intestinal metagenome and to investigate its potential role in formation of α-(1→4,6)-branched α-glucans from starch. The branching activity of purified GlgB was determined with six different starches and pure amylose by quantification of amylose after treatment. GlgB reduced the amylose content of all 6 starches and amylose by more than 85% and displayed a higher preference towards amylose. The observed activity on raw starch indicated a potential role in the primary starch degradation in the large intestine as an enzyme that solubilizes amylose. The oligosaccharide profile showed an increased concentration of oligosaccharide introduced by GlgB that is not hydrolyzed by intestinal enzymes. This corresponded to a reduced in vitro starch digestibility when compared to untreated starch. The study improves our understanding of colonic starch fermentation and may allow starch conversion to produce food products with reduced digestibility and improved quality.}, }
@article {pmid36838497, year = {2023}, author = {Habibi, N and Uddin, S and Al-Sarawi, H and Aldhameer, A and Shajan, A and Zakir, F and Abdul Razzack, N and Alam, F}, title = {Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020531}, pmid = {36838497}, issn = {2076-2607}, abstract = {Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.}, }
@article {pmid36838473, year = {2023}, author = {Bastos, TS and Souza, CMM and Legendre, H and Richard, N and Pilla, R and Suchodolski, JS and de Oliveira, SG and Lesaux, AA and Félix, AP}, title = {Effect of Yeast Saccharomyces cerevisiae as a Probiotic on Diet Digestibility, Fermentative Metabolites, and Composition and Functional Potential of the Fecal Microbiota of Dogs Submitted to an Abrupt Dietary Change.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020506}, pmid = {36838473}, issn = {2076-2607}, abstract = {The aim was to evaluate the effects of yeast probiotic on diet digestibility, fermentative metabolites, and fecal microbiota of dogs submitted to dietary change. Sixteen dogs were divided into two groups of eight dogs each: control, without, and with probiotic, receiving 0.12 g/dog/day of live Saccharomyces cerevisiae yeast. The dogs were fed a lower protein and fiber diet for 21 days and then changed to a higher protein and fiber diet until day 49. Yeast supplementation did not statistically influence diet digestibility. The probiotic group had a lower fecal concentration of total biogenic amines (days 21 and 49), ammonia (day 23), and aromatic compounds and a higher fecal concentration of butyrate (p < 0.05). The probiotic group showed a lower dysbiosis index, a higher abundance (p < 0.05) of Bifidobacterium (days 35 and 49) and Turicibacter, and a lower abundance of Lactobacillus and E. coli (p < 0.05). Beta diversity demonstrated a clear differentiation in the gut microbiota between the control and probiotic groups on day 49. The control group showed upregulation in genes related to virulence factors, antibiotic resistance, and osmotic stress. The results indicated that the live yeast evaluated can have beneficial effects on intestinal functionality of dogs.}, }
@article {pmid36838462, year = {2023}, author = {Shi, W and Tang, S and Zhang, S}, title = {Microbiome of High-Rank Coal Reservoirs in the High-Production Areas of the Southern Qinshui Basin.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020497}, pmid = {36838462}, issn = {2076-2607}, abstract = {To study the distribution features of microorganisms in distinct hydrological areas of the southern Qinshui Basin, C-N-S microorganisms were studied using 16S RNA sequencing, metagenome sequencing and geochemical technologies, showing the high sensitivity of microorganisms to the hydrodynamic dynamics of coal. The hydrodynamic intensity of the #3 coal gradually decreased from the runoff areas to the stagnant areas. The stagnant zones have higher reservoir pressure, methane content, δ[13]CDIC and TDS and lower SO4[2-], Fe[3+] and NO3[-] concentrations than the runoff areas. C-N-S-cycling microorganisms, including those engaged in methanogenesis, nitrate respiration, fermentation, nitrate reduction, dark oxidation of sulfur compounds, sulfate respiration, iron respiration, chlorate reduction, aromatic compound degradation, denitrification, ammonification and nitrogen fixation, were more abundant in the stagnant areas. The relative abundance of C-N-S functional genes, including genes related to C metabolism (e.g., mcr, mer, mtr, fwd and mtd), N metabolism (e.g., nifDKH, nirK, narGHI, nosZ, amoB, norC and napAB) and sulfur metabolism (e.g., dsrAB and PAPSS), increased in the stagnant zones, indicating that there was active microbiological C-N-S cycling in the stagnant areas. The degradation and fermentation of terrestrial plant organic carbon and coal seam organic matter could provide substrates for methanogens, while nitrogen fixation and nitrification can provide nitrogen for methanogens, which are all favorable factors for stronger methanogenesis in stagnant areas. The coal in the study area is currently in the secondary biogenic gas generation stage because of the rising of the strata, which recharges atmospheric precipitation. The random forest model shows that the abundance of C-N-S microorganisms and genes could be used to distinguish different hydrological zones in coal reservoirs. Since stagnant zones are usually high-gas-bearing zones and high-production areas of CBM exploration, these microbiological indicators can be used as effective parameters to identify high-production-potential zones. In addition, nitrate respiration and sulfate respiration microorganisms consumed NO3[-] and SO4[2-], causing a decrease in the content of these two ions in the stagnant areas.}, }
@article {pmid36838449, year = {2023}, author = {Cheatham, CN and Gustafson, KL and McAdams, ZL and Turner, GM and Dorfmeyer, RA and Ericsson, AC}, title = {Standardized Complex Gut Microbiomes Influence Fetal Growth, Food Intake, and Adult Body Weight in Outbred Mice.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020484}, pmid = {36838449}, issn = {2076-2607}, abstract = {Obesity places a tremendous burden on individual health and the healthcare system. The gut microbiome (GM) influences host metabolism and behaviors affecting body weight (BW) such as feeding. The GM of mice varies between suppliers and significantly influences BW. We sought to determine whether GM-associated differences in BW are associated with differences in intake, fecal energy loss, or fetal growth. Pair-housed mice colonized with a low or high microbial richness GM were weighed, and the total and BW-adjusted intake were measured at weaning and adulthood. Pups were weighed at birth to determine the effects of the maternal microbiome on fetal growth. Fecal samples were collected to assess the fecal energy loss and to characterize differences in the microbiome. The results showed that supplier-origin microbiomes were associated with profound differences in fetal growth and excessive BW-adjusted differences in intake during adulthood, with no detected difference in fecal energy loss. Agreement between the features of the maternal microbiome associated with increased birth weight here and in recent human studies supports the value of this model to investigate the mechanisms by which the maternal microbiome regulates offspring growth and food intake.}, }
@article {pmid36838393, year = {2023}, author = {Langlois, V and Girard, C and Vincent, WF and Culley, AI}, title = {A Tale of Two Seasons: Distinct Seasonal Viral Communities in a Thermokarst Lake.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020428}, pmid = {36838393}, issn = {2076-2607}, abstract = {Thermokarst lakes are important features of subarctic landscapes and are a substantial source of greenhouse gases, although the extent of gas produced varies seasonally. Microbial communities are responsible for the production of methane and CO2 but the "top down" forces that influence microbial dynamics (i.e., grazers and viruses) and how they vary temporally within these lakes are still poorly understood. The aim of this study was to examine viral diversity over time to elucidate the seasonal structure of the viral communities in thermokarst lakes. We produced virus-enriched metagenomes from a subarctic peatland thermokarst lake in the summer and winter over three years. The vast majority of vOTUs assigned to viral families belonged to Caudovirales (Caudoviricetes), notably the morphological groups myovirus, siphovirus and podovirus. We identified two distinct communities: a dynamic, seasonal community in the oxygenated surface layer during the summer and a stable community found in the anoxic water layer at the bottom of the lake in summer and throughout much of the water column in winter. Comparison with other permafrost and northern lake metagenomes highlighted the distinct composition of viral communities in this permafrost thaw lake ecosystem.}, }
@article {pmid36838385, year = {2023}, author = {Becker, D and Popp, D and Bonk, F and Kleinsteuber, S and Harms, H and Centler, F}, title = {Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020420}, pmid = {36838385}, issn = {2076-2607}, abstract = {Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). Methanothrix showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when Methanosarcina took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species-15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes.}, }
@article {pmid36838375, year = {2023}, author = {Lloyd, AW and Percival, D and Langille, MGI and Yurgel, SN}, title = {Changes to Soil Microbiome Resulting from Synergetic Effects of Fungistatic Compounds Pyrimethanil and Fluopyram in Lowbush Blueberry Agriculture, with Nine Fungicide Products Tested.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020410}, pmid = {36838375}, issn = {2076-2607}, abstract = {Lowbush blueberries (Vaccinium spp.) are a crop of economic significance to Atlantic Canada, Quebec, and Maine. The fruit is produced by the management of naturally occurring plant populations. The plants have an intimate relationship with the soil microbiome and depend on it for their health and productivity. Fungicides are an important tool in combatting disease pressure but pose a potential risk to soil health. In this study, amplicon sequencing was used to determine the effects of six fungistatic compounds both alone and in combination via nine commercially available fungicide products on the bacterial and fungal microbiomes associated with lowbush blueberries and to study whether these effects are reflected in crop outcomes and plant phenotypes. One fungicide, Luna Tranquility, a combination of fluopyram and pyrimethanil, was found to impart significant effects to fungal and bacterial community structure, fungal taxonomic abundances, and bacterial functions relative to control. The two fungicides which contained fluopyram and pyrimethanil as single ingredients (Velum Prime and Scala, respectively) did not induce significant changes in any of these regards. These results suggest the possibility that these microbiome changes are the result of the synergistic effect of fluopyram and pyrimethanil on soil microbiomes. While these results suggest a significant disruption to the soil microbiome, no corresponding changes to crop development and outcomes were noted. Ultimately, the majority of the fungicides analysed in this trial did not produce significant changes to the soil microbiome relative to the untreated group (UTG). However, one of the fungicide treatments, Luna Tranquility, did produce significant changes to the soil ecosystem that could have longer-term effects on soil health and its future use may merit additional investigation onto its ecotoxicological properties.}, }
@article {pmid36838367, year = {2023}, author = {Lumbreras-Iglesias, P and Sabater, C and Fernández Moreno, A and López de Ugarriza, P and Fernández-Verdugo, A and Margolles, A and Rodicio, MR and Bernal, T and Fernández, J}, title = {Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales in Culture Negative Patients Recovered from Acute Leukemia.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020402}, pmid = {36838367}, issn = {2076-2607}, abstract = {Patients diagnosed with acute leukemia (AL) have a weakened immune system. Infections acquired by these patients are cause for concern and especially worrisome when Gram-negative multidrug-resistant (MDR) bacteria are involved, as they are difficult to treat, especially in the case of ESBL- and/or carbapenemase-producing Enterobacterales. Culture-based approaches have been relied on over the past decades as the method of choice for the early detection of gut colonization by MDR Gram-negative bacteria. However, various studies have indicated its limited sensitivity, underlining the need for new screening procedures in onco-hematological patients. Here, we evaluated a shotgun metagenomics approach to detect ESBL- and/or carbapenemase-producing Enterobacterales in the gut of 28 patients who had recovered from AL, which were previously colonized by these bacteria but cured at the time of sampling, as judged by culture-based methods. No ESBL or carbapenemase determinants were detected among the many resistance genes found by the metagenomics approach, supporting that patients were truly decolonized, with considerable consequences for their future clinical management. Due to the relatively low number of patients available for the present investigation, further studies should be conducted to support the utility and applicability of metagenomics for the routine screening of MDR bacteria in onco-hematological patients.}, }
@article {pmid36838323, year = {2023}, author = {Zhou, X and Ma, Y and Yang, C and Zhao, Z and Ding, Y and Zhang, Y and Wang, P and Zhao, L and Li, C and Su, Z and Wang, X and Ming, W and Zeng, L and Kang, X}, title = {Rumen and Fecal Microbiota Characteristics of Qinchuan Cattle with Divergent Residual Feed Intake.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020358}, pmid = {36838323}, issn = {2076-2607}, abstract = {Residual feed intake (RFI) is one of the indicators of feed efficiency. To investigate the microbial characteristics and differences in the gastrointestinal tract of beef cattle with different RFI, a metagenome methodology was used to explore the characteristics of the rumen and fecal microbiota in 10 Qinchuan cattle (five in each of the extremely high and extremely low RFI groups). The results of taxonomic annotation revealed that Bacteroidetes and Firmicutes were the most dominant phyla in rumen and feces. Prevotella was identified as a potential biomarker in the rumen of the LRFI group by the LEfSe method, while Turicibacter and Prevotella might be potential biomarkers of the HRFI and LRFI group in feces, respectively. Functional annotation revealed that the microbiota in the rumen of the HRFI group had a greater ability to utilize dietary polysaccharides and dietary protein. Association analysis of rumen microbes (genus level) with host genes revealed that microbiota including Prevotella, Paraprevotella, Treponema, Oscillibacter, and Muribaculum, were significantly associated with differentially expressed genes regulating RFI. This study discovered variances in the microbial composition of rumen and feces of beef cattle with different RFIs, demonstrating that differences in microbes may play a critical role in regulating the bovine divergent RFI phenotype variations.}, }
@article {pmid36838276, year = {2023}, author = {Petrilli, R and Fabbretti, A and Cerretani, A and Pucci, K and Pagliaretta, G and Picciolini, M and Napolioni, V and Falconi, M}, title = {Selection, Identification and Functional Performance of Ammonia-Degrading Microbial Communities from an Activated Sludge for Landfill Leachate Treatment.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020311}, pmid = {36838276}, issn = {2076-2607}, abstract = {The increasing amounts of municipal solid waste and their management in landfills caused an increase in the production of leachate, a liquid formed by the percolation of rainwater through the waste. Leachate creates serious problems to municipal wastewater treatment plants; indeed, its high levels of ammonia are toxic for bacterial cells and drastically reduce the biological removal of nitrogen by activated sludge. In the present work, we studied, using a metagenomic approach based on next-generation sequencing (NGS), the microbial composition of sludge in the municipal wastewater treatment plant of Porto Sant'Elpidio (Italy). Through activated sludge enrichment experiments based on the Repetitive Re-Inoculum Assay, we were able to select and identify a minimal bacterial community capable of degrading high concentrations of ammonium (NH4[+]-N ≅ 350 mg/L) present in a leachate-based medium. The analysis of NGS data suggests that seven families of bacteria (Alcaligenaceae, Nitrosomonadaceae, Caulobacteraceae, Xanthomonadaceae, Rhodanobacteraceae, Comamonadaceae and Chitinophagaceae) are mainly responsible for ammonia oxidation. Furthermore, we isolated from the enriched sludge three genera (Klebsiella sp., Castellaniella sp. and Acinetobacter sp.) capable of heterotrophic nitrification coupled with aerobic denitrification. These bacteria released a trace amount of both nitrite and nitrate possibly transforming ammonia into gaseous nitrogen. Our findings represent the starting point to produce an optimized microorganisms's mixture for the biological removal of ammonia contained in leachate.}, }
@article {pmid36838234, year = {2023}, author = {Arsyadi, A and Guo, Y and Ebihara, A and Sakagami, N and Sakoda, M and Tago, K and Kamijo, T and Ohta, H and Nishizawa, T}, title = {A Nitrate-Transforming Bacterial Community Dominates in the Miscanthus Rhizosphere on Nitrogen-Deficient Volcanic Deposits of Miyake-jima.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/microorganisms11020260}, pmid = {36838234}, issn = {2076-2607}, abstract = {The perennial gramineous grass Miscanthus condensatus functions as a major pioneer plant in colonizing acidic volcanic deposits on Miyake-jima, Japan, despite a lack of nitrogen nutrients. The nitrogen cycle in the rhizosphere is important for the vigorous growth of M. condensatus in this unfavorable environment. In the present study, we identified the nitrogen-cycling bacterial community in the M. condensatus rhizosphere on these volcanic deposits using a combination of metagenomics and culture-based analyses. Our results showed a large number of functional genes related to denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in the rhizosphere, indicating that nitrate-transforming bacteria dominated the rhizosphere biome. Furthermore, nitrite reductase genes (i.e., nirK and nirS) related to the denitrification and those genes related to DNRA (i.e., nirB and nrfA) were mainly annotated to the classes Alpha-proteobacteria, Beta-proteobacteria, and Gamma-proteobacteria. A total of 304 nitrate-succinate-stimulated isolates were obtained from the M. condensatus rhizosphere and were classified into 34 operational taxonomic units according to amplified 16S rRNA gene restriction fragment pattern analysis. Additionally, two strains belonging to the genus Cupriavidus in the class Beta-proteobacteria showed a high in vitro denitrifying activity; however, metagenomic results indicated that the DNRA-related rhizobacteria appeared to take a major role in the nitrogen cycle of the M. condensatus rhizosphere in recent Miyake-jima volcanic deposits. This study elucidates the association between the Miscanthus rhizosphere and the nitrate-reducing bacterial community on newly placed volcanic deposits, which furthers our understanding of the transformation of nitrogen nutrition involved in the early development of vegetation.}, }
@article {pmid36837868, year = {2023}, author = {Song, F and Xu, Y and Peng, P and Li, H and Zheng, R and Zhang, H and Han, Y and Weng, Q and Yuan, Z}, title = {Seasonal Changes in the Structure and Function of Gut Microbiota in the Muskrat (Ondatra zibethicus).}, journal = {Metabolites}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/metabo13020248}, pmid = {36837868}, issn = {2218-1989}, abstract = {The gut microbiota plays a crucial role in the nutrition, metabolism, and immune function of the host animal. The muskrat (Ondatra zibethicus) is a typical seasonal breeding animal. The present study performed a metagenomic analysis of cecum contents from muskrats in the breeding and non-breeding seasons. The results indicated that the breeding muskrats and non-breeding muskrats differed in gut microbiota structure and function. During the breeding season, the relative abundance of phylum Bacteroidetes, genus Prevotella, and genus Alistipes increased, while the relative abundance of phylum Firmicutes and phylum Actinobacteria decreased. The muskrat gut microbiota was enriched in the metabolism-related pathways, especially amino acid and vitamin metabolism, and genetically related metabolites in the breeding season. We presumed that the muskrat gut microbiota might seasonally change to secure reproductive activity and satisfy the metabolic demands of different seasons. This study could explore potential mechanisms by which gut microbiota affects reproduction. Moreover, this study may provide a new theoretical basis for the management of muskrat captive breeding.}, }
@article {pmid36836616, year = {2023}, author = {Tarbeeva, S and Kozlova, A and Sarygina, E and Kiseleva, O and Ponomarenko, E and Ilgisonis, E}, title = {Food for Thought: Proteomics for Meat Safety.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/life13020255}, pmid = {36836616}, issn = {2075-1729}, abstract = {Foodborne bacteria interconnect food and human health. Despite significant progress in food safety regulation, bacterial contamination is still a serious public health concern and the reason for significant commercial losses. The screening of the microbiome in meals is one of the main aspects of food production safety influencing the health of the end-consumers. Our research provides an overview of proteomics findings in the field of food safety made over the last decade. It was believed that proteomics offered an accurate snapshot of the complex networks of the major biological machines called proteins. The proteomic methods for the detection of pathogens were armed with bioinformatics algorithms, allowing us to map the data onto the genome and transcriptome. The mechanisms of the interaction between bacteria and their environment were elucidated with unprecedented sensitivity, specificity, and depth. Using our web-based tool ScanBious for automated publication analysis, we analyzed over 48,000 scientific articles on antibiotic and disinfectant resistance and highlighted the benefits of proteomics for the food safety field. The most promising approach to studying safety in food production is the combination of classical genomic and metagenomic approaches and the advantages provided by proteomic methods with the use of panoramic and targeted mass spectrometry.}, }
@article {pmid36836275, year = {2023}, author = {Singh, G}, title = {Linking Lichen Metabolites to Genes: Emerging Concepts and Lessons from Molecular Biology and Metagenomics.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {2}, pages = {}, doi = {10.3390/jof9020160}, pmid = {36836275}, issn = {2309-608X}, abstract = {Lichen secondary metabolites have tremendous pharmaceutical and industrial potential. Although more than 1000 metabolites have been reported from lichens, less than 10 have been linked to the genes coding them. The current biosynthetic research focuses strongly on linking molecules to genes as this is fundamental to adapting the molecule for industrial application. Metagenomic-based gene discovery, which bypasses the challenges associated with culturing an organism, is a promising way forward to link secondary metabolites to genes in non-model, difficult-to-culture organisms. This approach is based on the amalgamation of the knowledge of the evolutionary relationships of the biosynthetic genes, the structure of the target molecule, and the biosynthetic machinery required for its synthesis. So far, metagenomic-based gene discovery is the predominant approach by which lichen metabolites have been linked to their genes. Although the structures of most of the lichen secondary metabolites are well-documented, a comprehensive review of the metabolites linked to their genes, strategies implemented to establish this link, and crucial takeaways from these studies is not available. In this review, I address the following knowledge gaps and, additionally, provide critical insights into the results of these studies, elaborating on the direct and serendipitous lessons that we have learned from them.}, }
@article {pmid36835562, year = {2023}, author = {von Eyben, FE and Kristiansen, K and Kapp, DS and Hu, R and Preda, O and Nogales, FF}, title = {Epigenetic Regulation of Driver Genes in Testicular Tumorigenesis.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, doi = {10.3390/ijms24044148}, pmid = {36835562}, issn = {1422-0067}, abstract = {In testicular germ cell tumor type II (TGCT), a seminoma subtype expresses an induced pluripotent stem cell (iPSC) panel with four upregulated genes, OCT4/POU5F1, SOX17, KLF4, and MYC, and embryonal carcinoma (EC) has four upregulated genes, OCT4/POU5F1, SOX2, LIN28, and NANOG. The EC panel can reprogram cells into iPSC, and both iPSC and EC can differentiate into teratoma. This review summarizes the literature on epigenetic regulation of the genes. Epigenetic mechanisms, such as methylations of cytosines on the DNA string and methylations and acetylations of histone 3 lysines, regulate expression of these driver genes between the TGCT subtypes. In TGCT, the driver genes contribute to well-known clinical characteristics and the driver genes are also important for aggressive subtypes of many other malignancies. In conclusion, epigenetic regulation of the driver genes are important for TGCT and for oncology in general.}, }
@article {pmid36835363, year = {2023}, author = {Smythe, P and Wilkinson, HN}, title = {The Skin Microbiome: Current Landscape and Future Opportunities.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, doi = {10.3390/ijms24043950}, pmid = {36835363}, issn = {1422-0067}, abstract = {Our skin is the largest organ of the body, serving as an important barrier against the harsh extrinsic environment. Alongside preventing desiccation, chemical damage and hypothermia, this barrier protects the body from invading pathogens through a sophisticated innate immune response and co-adapted consortium of commensal microorganisms, collectively termed the microbiota. These microorganisms inhabit distinct biogeographical regions dictated by skin physiology. Thus, it follows that perturbations to normal skin homeostasis, as occurs with ageing, diabetes and skin disease, can cause microbial dysbiosis and increase infection risk. In this review, we discuss emerging concepts in skin microbiome research, highlighting pertinent links between skin ageing, the microbiome and cutaneous repair. Moreover, we address gaps in current knowledge and highlight key areas requiring further exploration. Future advances in this field could revolutionise the way we treat microbial dysbiosis associated with skin ageing and other pathologies.}, }
@article {pmid36834289, year = {2023}, author = {Zhao, F and Wang, B and Huang, K and Yin, J and Ren, X and Wang, Z and Zhang, XX}, title = {Correlations among Antibiotic Resistance Genes, Mobile Genetic Elements and Microbial Communities in Municipal Sewage Treatment Plants Revealed by High-Throughput Sequencing.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {4}, pages = {}, doi = {10.3390/ijerph20043593}, pmid = {36834289}, issn = {1660-4601}, abstract = {Municipal sewage treatment plants (MSTPs) are environmental pools for antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which is cause for growing environmental-health concerns. In this study, the effects of different wastewater treatment processes on microbial antibiotic resistance in four MSTPs were investigated. PCR, q-PCR, and molecular cloning integrally indicated that the tetracycline resistance (tet) genes significantly reduced after activated-sludge treatment. Illumina high-throughput sequencing revealed that the broad-spectrum profile of ARGs and mobile element genes (MGEs) were also greatly decreased by one order of magnitude via activated sludge treatment and were closely associated with each other. Correlations between ARGs and bacterial communities showed that potential ARB, such as Acinetobacter, Bacteroides, and Cloaibacterium, were removed by the activated-sludge process. Sedimentation processes cannot significantly affect the bacterial structure, resulting in the relative abundance of ARGs, MGEs, and ARB in second-clarifier effluent water being similar to activated sludge. A comprehensive study of ARGs associated with MGEs and bacterial structure might be technologically guided for activated sludge design and operation in the MSTPs, to purposefully control ARGs carried by pathogenic hosts and mobility.}, }
@article {pmid36833289, year = {2023}, author = {Winder, JC and Boulton, W and Salamov, A and Eggers, SL and Metfies, K and Moulton, V and Mock, T}, title = {Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/genes14020363}, pmid = {36833289}, issn = {2073-4425}, abstract = {Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural diversity in natural microbial communities is limited. Here, we used samples from sea ice and sea water collected in the central Arctic Ocean as part of the MOSAiC expedition for metagenome sequencing and the subsequent analyses of metagenome-assembled genomes (MAGs). By linking structurally diverse IBPs to particular environments and potential functions, we reveal that IBP sequences are enriched in interior ice, have diverse genomic contexts and cluster taxonomically. Their diverse protein structures may be a consequence of domain shuffling, leading to variable combinations of protein domains in IBPs and probably reflecting the functional versatility required to thrive in the extreme and variable environment of the central Arctic Ocean.}, }
@article {pmid36833250, year = {2023}, author = {ZeinEldin, RA and Ahmed, MM and Hassanein, WS and Elshafey, N and Sofy, AR and Hamedo, HA and Elnosary, ME}, title = {Diversity and Distribution Characteristics of Viruses from Soda Lakes.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/genes14020323}, pmid = {36833250}, issn = {2073-4425}, abstract = {Viruses are the most abundant living things and a source of genetic variation. Despite recent research, we know little about their biodiversity and geographic distribution. We used different bioinformatics tools, MG-RAST, genome detective web tools, and GenomeVx, to describe the first metagenomic examination of haloviruses in Wadi Al-Natrun. The discovered viromes had remarkably different taxonomic compositions. Most sequences were derived from double-stranded DNA viruses, especially from Myoviridae, Podoviridae, Siphoviridae, Herpesviridae, Bicaudaviridae, and Phycodnaviridae families; single-stranded DNA viruses, especially from the family Microviridae; and positive-strand RNA viruses, especially from the family Potyviridae. Additionally, our results showed that Myohalovirus chaoS9 has eight Contigs and is annotated to 18 proteins as follows: tail sheath protein, tco, nep, five uncharacterized proteins, HCO, major capsid protein, putative pro head protease protein, putative head assembly protein, CxxC motive protein, terl, HTH domain protein, and terS Exon 2. Additionally, Halorubrum phage CGphi46 has 19 proteins in the brine sample as follows: portal protein, 17 hypothetical proteins, major capsid protein, etc. This study reveals viral lineages, suggesting the Virus's global dispersal more than other microorganisms. Our study clarifies how viral communities are connected and how the global environment changes.}, }
@article {pmid36833230, year = {2023}, author = {Wiscovitch-Russo, RA and Santiago-Rodriguez, TM and Toranzos, GA}, title = {Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/genes14020303}, pmid = {36833230}, issn = {2073-4425}, abstract = {Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed.}, }
@article {pmid36831166, year = {2023}, author = {Yuan, Q and Wang, X and Li, Z and Guo, W and Cheng, H and Cao, Q}, title = {A Preliminary Study on Microbiota Characteristics of Bronchoalveolar Lavage Fluid in Patients with Pulmonary Nodules Based on Metagenomic Next-Generation Sequencing.}, journal = {Biomedicines}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/biomedicines11020631}, pmid = {36831166}, issn = {2227-9059}, abstract = {BACKGROUND: The characteristics and roles of microbes in the occurrence and development of pulmonary nodules are still unclear.<br><br>METHODS: We retrospectively analyzed the microbial mNGS results of BALF from 229 patients with pulmonary nodules before surgery, and performed a comparative analysis of lung flora between lung cancer and benign nodules according to postoperative pathology. The analysis also focused on investigating the characteristics of lung microbiota in lung adenocarcinomas with varying histopathology.<br><br>RESULTS: There were differences in lung microbiota between lung cancer and benign lung nodules. Bacterial diversity was lower in lung cancer than in benign lung nodules. Four species (Porphyromonas somerae, Corynebacterium accolens, Burkholderia cenocepacia and Streptococcus mitis) were enriched in lung cancer compared with the benign lung nodules. The areas under the ROC curves of these four species were all greater than 0.6, and the AUC of Streptococcus mitis was 0.702, which had the highest diagnostic value for differentiating lung cancer from benign lung diseases. The significantly enriched microbiota varied with the different pathological subtypes of lung adenocarcinoma. Streptococcus mitis, Burkholderia oklahomensis and Burkholderia latens displayed a trend of increasing from the benign lung disease group to the AIS group, MIA group and IAC group, whereas Lactobacillus plantarum showed a downward trend.<br><br>CONCLUSION: Changes in the abundance of lung microbiota are closely related to the development of infiltrating adenocarcinoma. Our findings provide new insights into the relationship between the changes in lung microbiota and the development of lung cancer.}, }
@article {pmid36830905, year = {2023}, author = {Mańkowska-Wierzbicka, D and Zuraszek, J and Wierzbicka, A and Gabryel, M and Mahadea, D and Baturo, A and Zakerska-Banaszak, O and Slomski, R and Skrzypczak-Zielinska, M and Dobrowolska, A}, title = {Alterations in Gut Microbiota Composition in Patients with COVID-19: A Pilot Study of Whole Hypervariable 16S rRNA Gene Sequencing.}, journal = {Biomedicines}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/biomedicines11020367}, pmid = {36830905}, issn = {2227-9059}, abstract = {It is crucial to consider the importance of the microbiome and the gut-lung axis in the context of SARS-CoV-2 infection. This pilot study examined the fecal microbial composition of patients with COVID-19 following a 3-month recovery. Using for the first time metagenomic analysis based on all hypervariable regions (V1-V9) of the 16S rRNA gene, we have identified 561 microbial species; however, 17 were specific only for the COVID-19 group (n = 8). The patients' cohorts revealed significantly greater alpha diversity of the gut microbiota compared to healthy controls (n = 14). This finding has been demonstrated by operational taxonomic units (OTUs) richness (p < 0.001) and Chao1 index (p < 0.01). The abundance of the phylum Verrucomicrobia was 30 times higher in COVID-19 patients compared to healthy subjects. Accordingly, this disproportion was also noted at other taxonomic levels: in the class Verrucomicrobiae, the family Verrucomicrobiaceae, and the genus Akkermansia. Elevated pathobionts such as Escherichia coli, Bilophila wadsworthia, and Parabacteroides distasonis were found in COVID-19 patients. Considering the gut microbiota's ability to disturb the immune response, our findings suggest the importance of the enteric microbiota in the course of SARS-CoV-2 infection. This pilot study shows that the composition of the microbial community may not be fully restored in individuals with SARS-CoV-2 following a 3-month recovery.}, }
@article {pmid36830830, year = {2023}, author = {Campbell, C and Kandalgaonkar, MR and Golonka, RM and Yeoh, BS and Vijay-Kumar, M and Saha, P}, title = {Crosstalk between Gut Microbiota and Host Immunity: Impact on Inflammation and Immunotherapy.}, journal = {Biomedicines}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/biomedicines11020294}, pmid = {36830830}, issn = {2227-9059}, abstract = {Gut microbes and their metabolites are actively involved in the development and regulation of host immunity, which can influence disease susceptibility. Herein, we review the most recent research advancements in the gut microbiota-immune axis. We discuss in detail how the gut microbiota is a tipping point for neonatal immune development as indicated by newly uncovered phenomenon, such as maternal imprinting, in utero intestinal metabolome, and weaning reaction. We describe how the gut microbiota shapes both innate and adaptive immunity with emphasis on the metabolites short-chain fatty acids and secondary bile acids. We also comprehensively delineate how disruption in the microbiota-immune axis results in immune-mediated diseases, such as gastrointestinal infections, inflammatory bowel diseases, cardiometabolic disorders (e.g., cardiovascular diseases, diabetes, and hypertension), autoimmunity (e.g., rheumatoid arthritis), hypersensitivity (e.g., asthma and allergies), psychological disorders (e.g., anxiety), and cancer (e.g., colorectal and hepatic). We further encompass the role of fecal microbiota transplantation, probiotics, prebiotics, and dietary polyphenols in reshaping the gut microbiota and their therapeutic potential. Continuing, we examine how the gut microbiota modulates immune therapies, including immune checkpoint inhibitors, JAK inhibitors, and anti-TNF therapies. We lastly mention the current challenges in metagenomics, germ-free models, and microbiota recapitulation to a achieve fundamental understanding for how gut microbiota regulates immunity. Altogether, this review proposes improving immunotherapy efficacy from the perspective of microbiome-targeted interventions.}, }
@article {pmid36830574, year = {2023}, author = {Roux, S and Fischer, MG and Hackl, T and Katz, LA and Schulz, F and Yutin, N}, title = {Updated Virophage Taxonomy and Distinction from Polinton-like Viruses.}, journal = {Biomolecules}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/biom13020204}, pmid = {36830574}, issn = {2218-273X}, abstract = {Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.}, }
@article {pmid36830527, year = {2023}, author = {Christodoulou, C and Mavrommatis, A and Loukovitis, D and Symeon, G and Dotas, V and Kotsampasi, B and Tsiplakou, E}, title = {Effect of Spirulina Dietary Supplementation in Modifying the Rumen Microbiota of Ewes.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/ani13040740}, pmid = {36830527}, issn = {2076-2615}, abstract = {Supplementing ruminant diets with microalgae, may prove an effective nutritional strategy to manipulate rumen microbiota. Forty-eight ewes were divided into four homogenous groups (n = 12) according to their fat-corrected milk yield (6%), body weight, age, and days in milk, and were fed individually with concentrate, alfalfa hay, and wheat straw. The concentrate of the control group (CON) had no Spirulina supplementation, while in the treated groups 5 (SP5), 10 (SP10), and 15 g (SP15) of Spirulina were supplemented as an additive in the concentrate. An initial screening using metagenomic next-generation sequencing technology was followed by RT-qPCR analysis for the targeting of specific microbes, which unveiled the main alterations of the rumen microbiota under the Spirulina supplementation levels. The relative abundance of Eubacterium ruminantium and Fibrobacter succinogenes in rumen fluid, as well as Ruminococcus albus in rumen solid fraction, were significantly increased in the SP15 group. Furthermore, the relative abundance of Prevotella brevis was significantly increased in the rumen fluid of the SP5 and SP10 groups. In contrast, the relative abundance of Ruminobacter amylophilus was significantly decreased in the rumen fluid of the SP10 compared to the CON group, while in the solid fraction it was significantly decreased in the SP groups. Moreover, the relative abundance of Selenomonas ruminantium was significantly decreased in the SP5 and SP15 groups, while the relative abundance of Streptococcus bovis was significantly decreased in the SP groups. Consequently, supplementing 15 g Spirulina/ewe/day increased the relative abundance of key cellulolytic species in the rumen, while amylolytic species were reduced only in the solid fraction.}, }
@article {pmid36830498, year = {2023}, author = {Hayashi, M and Shinozuka, Y and Kurumisawa, T and Yagisawa, T and Suenaga, N and Shimizu, Y and Suzuki, N and Kawai, K}, title = {Effects of Intramammary Antimicrobial Treatment on the Milk Microbiota Composition in Mild Clinical Bovine Mastitis Caused by Gram-Positive Bacteria.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/ani13040713}, pmid = {36830498}, issn = {2076-2615}, abstract = {The purpose of this study was to clarify the effects of antimicrobial treatment for mild mastitis caused by Gram-positive bacteria on the milk microbiota in dairy cattle. Sixteen quarters of sixteen cows with mild clinical mastitis from the same herd were included in the study. On the day of onset (day 0), the cows were randomly allocated to a no-treatment (NT; n = 10) group or an intramammary antimicrobial treatment (AMT) group that received AMT starting on day 0 (AMT-AMT group; n = 6). The next day (day 1), the cows in the NT group were randomly allocated into an NT group (NT-NT group; n = 3) that received no treatment or an AMT group that received AMT starting on day 1 (NT-AMT group; n = 7). Milk samples were collected on days 0, 1, 3 and 7, and the milk microbiota of each sample was comprehensively analyzed via 16S rRNA gene amplicon sequencing of the milk DNA. During the treatment period, the milk microbiota of the NT-NT group did not change, but those of the NT-AMT and AMT-AMT groups changed significantly on days three and seven. Thus, the use of antimicrobials for mild mastitis caused by Gram-positive bacteria changes the milk microbiota composition.}, }
@article {pmid36830429, year = {2023}, author = {Tardiolo, G and Romeo, O and Zumbo, A and Di Marsico, M and Sutera, AM and Cigliano, RA and Paytuví, A and D'Alessandro, E}, title = {Characterization of the Nero Siciliano Pig Fecal Microbiota after a Liquid Whey-Supplemented Diet.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {4}, pages = {}, doi = {10.3390/ani13040642}, pmid = {36830429}, issn = {2076-2615}, abstract = {The utilization of dairy by-products as animal feed, especially in swine production, is a strategy to provide functional ingredients to improve gut health. This study explored the potential effect of a liquid whey-supplemented diet on the fecal microbiota of eleven pigs belonging to the Nero Siciliano breed. Five pigs were assigned to the control group and fed with a standard formulation feed, whereas six pigs were assigned to the experimental group and fed with the same feed supplemented with liquid whey. Fecal samples were collected from each individual before the experimental diet (T0), and one (T1) and two (T2) months after the beginning of the co-feed supplementation. Taxonomic analysis, based on the V3-V4 region of the bacterial 16S rRNA, showed that pig feces were populated by a complex microbial community with a remarkable abundance of Firmicutes, Bacteroidetes, and Spirochaetes phyla and Prevotella, Lactobacillus, Clostridium, and Treponema genera. Alpha and beta diversity values suggested that the experimental diet did not significantly affect the overall fecal microbiota diversity. However, analysis of abundance at different time points revealed significant variation in several bacterial genera, suggesting that the experimental diet potentially affected some genera of the microbial community.}, }
@article {pmid36830296, year = {2023}, author = {Dobiáš, R and Stevens, DA and Havlíček, V}, title = {Current and Future Pathways in Aspergillus Diagnosis.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/antibiotics12020385}, pmid = {36830296}, issn = {2079-6382}, abstract = {Aspergillus fumigatus has been designated by the World Health Organization as a critical priority fungal pathogen. Some commercially available diagnostics for many forms of aspergillosis rely on fungal metabolites. These encompass intracellular molecules, cell wall components, and extracellular secretomes. This review summarizes the shortcomings of antibody tests compared to tests of fungal products in body fluids and highlights the application of β-d-glucan, galactomannan, and pentraxin 3 in bronchoalveolar lavage fluids. We also discuss the detection of nucleic acids and next-generation sequencing, along with newer studies on Aspergillus metallophores.}, }
@article {pmid36830277, year = {2023}, author = {Lüftinger, L and Májek, P and Rattei, T and Beisken, S}, title = {Metagenomic Antimicrobial Susceptibility Testing from Simulated Native Patient Samples.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/antibiotics12020366}, pmid = {36830277}, issn = {2079-6382}, abstract = {Genomic antimicrobial susceptibility testing (AST) has been shown to be accurate for many pathogens and antimicrobials. However, these methods have not been systematically evaluated for clinical metagenomic data. We investigate the performance of in-silico AST from clinical metagenomes (MG-AST). Using isolate sequencing data from a multi-center study on antimicrobial resistance (AMR) as well as shotgun-sequenced septic urine samples, we simulate over 2000 complicated urinary tract infection (cUTI) metagenomes with known resistance phenotype to 5 antimicrobials. Applying rule-based and machine learning-based genomic AST classifiers, we explore the impact of sequencing depth and technology, metagenome complexity, and bioinformatics processing approaches on AST accuracy. By using an optimized metagenomics assembly and binning workflow, MG-AST achieved balanced accuracy within 5.1% of isolate-derived genomic AST. For poly-microbial infections, taxonomic sample complexity and relatedness of taxa in the sample is a key factor influencing metagenomic binning and downstream MG-AST accuracy. We show that the reassignment of putative plasmid contigs by their predicted host range and investigation of whole resistome capabilities improved MG-AST performance on poly-microbial samples. We further demonstrate that machine learning-based methods enable MG-AST with superior accuracy compared to rule-based approaches on simulated native patient samples.}, }
@article {pmid36830274, year = {2023}, author = {Olías-Molero, AI and Botías, P and Cuquerella, M and García-Cantalejo, J and Barcia, E and Torrado, S and Torrado, JJ and Alunda, JM}, title = {Effect of Clindamycin on Intestinal Microbiome and Miltefosine Pharmacology in Hamsters Infected with Leishmania infantum.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/antibiotics12020362}, pmid = {36830274}, issn = {2079-6382}, abstract = {Visceral leishmaniasis (VL), a vector-borne parasitic disease caused by Leishmania donovani and L. infantum (Kinetoplastida), affects humans and dogs, being fatal unless treated. Miltefosine (MIL) is the only oral medication for VL and is considered a first choice drug when resistance to antimonials is present. Comorbidity and comedication are common in many affected patients but the relationship between microbiome composition, drugs administered and their pharmacology is still unknown. To explore the effect of clindamycin on the intestinal microbiome and the availability and distribution of MIL in target organs, Syrian hamsters (120-140 g) were inoculated with L. infantum (10[8] promastigotes/animal). Infection was maintained for 16 weeks, and the animals were treated with MIL (7 days, 5 mg/kg/day), clindamycin (1 mg/kg, single dose) + MIL (7 days, 5 mg/kg/day) or kept untreated. Infection was monitored by ELISA and fecal samples (16 wpi, 18 wpi, end point) were analyzed to determine the 16S metagenomic composition (OTUs) of the microbiome. MIL levels were determined by LC-MS/MS in plasma (24 h after the last treatment; end point) and target organs (spleen, liver) (end point). MIL did not significantly affect the composition of intestinal microbiome, but clindamycin provoked a transient albeit significant modification of the relative abundance of 45% of the genera, including Ruminococcaceae UCG-014, Ruminococcus 2; Bacteroides and (Eubacterium) ruminantium group, besides its effect on less abundant phyla and families. Intestinal dysbiosis in the antibiotic-treated animals was associated with significantly lower levels of MIL in plasma, though not in target organs at the end of the experiment. No clear relationship between microbiome composition (OTUs) and pharmacological parameters was found.}, }
@article {pmid36830245, year = {2023}, author = {Ordine, JVW and de Souza, GM and Tamasco, G and Virgilio, S and Fernandes, AFT and Silva-Rocha, R and Guazzaroni, ME}, title = {Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/antibiotics12020334}, pmid = {36830245}, issn = {2079-6382}, abstract = {Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities' structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.}, }
@article {pmid36830206, year = {2023}, author = {Fisher, CR and Patel, R}, title = {Profiling the Immune Response to Periprosthetic Joint Infection and Non-Infectious Arthroplasty Failure.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/antibiotics12020296}, pmid = {36830206}, issn = {2079-6382}, abstract = {Arthroplasty failure is a major complication of joint replacement surgery. It can be caused by periprosthetic joint infection (PJI) or non-infectious etiologies, and often requires surgical intervention and (in select scenarios) resection and reimplantation of implanted devices. Fast and accurate diagnosis of PJI and non-infectious arthroplasty failure (NIAF) is critical to direct medical and surgical treatment; differentiation of PJI from NIAF may, however, be unclear in some cases. Traditional culture, nucleic acid amplification tests, metagenomic, and metatranscriptomic techniques for microbial detection have had success in differentiating the two entities, although microbiologically negative apparent PJI remains a challenge. Single host biomarkers or, alternatively, more advanced immune response profiling-based approaches may be applied to differentiate PJI from NIAF, overcoming limitations of microbial-based detection methods and possibly, especially with newer approaches, augmenting them. In this review, current approaches to arthroplasty failure diagnosis are briefly overviewed, followed by a review of host-based approaches for differentiation of PJI from NIAF, including exciting futuristic combinational multi-omics methodologies that may both detect pathogens and assess biological responses, illuminating causes of arthroplasty failure.}, }
@article {pmid36830128, year = {2023}, author = {Perikleous, EP and Gkentzi, D and Bertzouanis, A and Paraskakis, E and Sovtic, A and Fouzas, S}, title = {Antibiotic Resistance in Patients with Cystic Fibrosis: Past, Present, and Future.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/antibiotics12020217}, pmid = {36830128}, issn = {2079-6382}, abstract = {Patients with cystic fibrosis (CF) are repeatedly exposed to antibiotics, especially during the pulmonary exacerbations of the disease. However, the available therapeutic strategies are frequently inadequate to eradicate the involved pathogens and most importantly, facilitate the development of antimicrobial resistance (AMR). The evaluation of AMR is demanding; conventional culture-based susceptibility-testing techniques cannot account for the lung microenvironment and/or the adaptive mechanisms developed by the pathogens, such as biofilm formation. Moreover, features linked to modified pharmaco-kinetics and pulmonary parenchyma penetration make the dosing of antibiotics even more challenging. In this review, we present the existing knowledge regarding AMR in CF, we shortly review the existing therapeutic strategies, and we discuss the future directions of antimicrobial stewardship. Due to the increasing difficulty in eradicating strains that develop AMR, the appropriate management should rely on targeting the underlying resistance mechanisms; thus, the interest in novel, molecular-based diagnostic tools, such as metagenomic sequencing and next-generation transcriptomics, has increased exponentially. Moreover, since the development of new antibiotics has a slow pace, the design of effective treatment strategies to eradicate persistent infections represents an urgency that requires consorted work. In this regard, both the management and monitoring of antibiotics usage are obligatory and more relevant than ever.}, }
@article {pmid36829425, year = {2023}, author = {Fernandes, P and Afonso, IM and Pereira, J and Rocha, R and Rodrigues, AS}, title = {Epiphitic Microbiome of Alvarinho Wine Grapes from Different Geographic Regions in Portugal.}, journal = {Biology}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/biology12020146}, pmid = {36829425}, issn = {2079-7737}, abstract = {Geographic location and, particularly, soil and climate exert influence on the typicality of a wine from a specific region, which is often justified by the terroir, and these factors also influence the epiphytic flora associated with the surface of the grape berries. In the present study, the microbiome associated with the surface of berries obtained from ten vineyards of the Alvarinho variety located in different geographical locations in mainland Portugal was determined and analyzed. The removal of microbial flora from the surface of the berries was carried out by washing and sonication, after which the extraction and purification of the respective DNA was carried out. High-throughput short amplicon sequencing of the fungal ITS region and the bacterial 16S region was performed, allowing for the determination of the microbial consortium associated with Alvarinho wine grapes. Analysis of α-diversity demonstrated that parcels from the Monção and Melgaço sub-region present a significantly (p < 0.05) lower fungal diversity and species richness when compared to the plots analyzed from other regions/sub-regions. The ubiquitous presence of Metschnikowia spp., a yeast with enologic potential interest in all parcels from Monção and Melgaço, was also observed.}, }
@article {pmid36829171, year = {2023}, author = {Huang, L and Xu, S and Huang, Z and Chen, Y and Xu, N and Xie, B}, title = {Risk factors associated with Pneumocystis jirovecii pneumonia in non-HIV immunocompromised patients and co-pathogens analysis by metagenomic next-generation sequencing.}, journal = {BMC pulmonary medicine}, volume = {23}, number = {1}, pages = {72}, pmid = {36829171}, issn = {1471-2466}, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is one of the most common opportunistic infections in immunocompromised patients. However, the accurate prediction of the development of PJP in non-HIV immunocompromised patients is still unclear.<br><br>METHODS: Non-HIV immunocompromised patients confirmed diagnosis of PJP by the clinical symptoms, chest computed tomography and etiological results of metagenomic next-generation sequencing (mNGS) were enrolled as observation group. Another group of matched non-HIV immunocompromised patients with non-PJP pneumonia were enrolled to control group. The risk factors for the development of PJP and the co-pathogens in the bronchoalveolar lavage fluid (BALF) detected by mNGS were analyzed.&#xa0; RESULTS: A total of 67 (33 PJP, 34 non-PJP) participants were enrolled from Fujian Provincial Hospital. The ages, males and underlying illnesses were not significantly different between the two groups. Compared to non-PJP patients, PJP patients were more tends to have the symptoms of fever and dyspnea. The LYM and ALB were significantly lower in PJP patients than in non-PJP patients. Conversely, LDH and serum BDG in PJP patients were significantly higher than in non-PJP controls. For immunological indicators, the levels of immunoglobulin A, G, M and complement C3, C4, the numbers of T, B, and NK cells, had no statistical difference between these two groups. Logistic multivariate analysis showed that concomitant use of corticosteroids and immunosuppressant (OR 14.146, P&#x2009;=&#x2009;0.004) and the lymphocyte counts&#x2009;<&#x2009;0.7&#x2009;&#xd7;&#x2009;10[9]/L (OR 6.882, P&#x2009;=&#x2009;0.011) were risk factors for the development of PJP in non-HIV immunocompromised patients. 81.82% (27/33) and 64.71% (22/34) mixed infections were identified by mNGS in the PJP group and non-PJP group separately. CMV, EBV and Candida were the leading co-pathogens in PJP patients. The percentages of CMV and EBV identified by mNGS in PJP group were significantly higher than those in the control group(p&#x2009;<&#x2009;0.005).&#xa0; CONCLUSIONS: Clinicians should pay close attention to the development of PJP in non-HIV immunocompromised patients who possess the risk factors of concomitant use of corticosteroids and immunosuppressant and the lymphocyte counts&#x2009;<&#x2009;0.7&#x2009;&#xd7;&#x2009;10[9]/L. Prophylaxis for PJP cannot rely solely on CD4[+] T counts in non-HIV immunocompromised patients. Whether CMV infection increases the risk of PJP remains to be further investigated.}, }
@article {pmid36828854, year = {2023}, author = {Yu, H and Xiong, L and Li, Y and Wei, Y and Zhang, Q and Li, H and Chen, W and Ji, X}, title = {Genetic diversity of virus auxiliary metabolism genes associated with phosphorus metabolism in Napahai plateau wetland.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3250}, pmid = {36828854}, issn = {2045-2322}, abstract = {Viruses play important roles in ecosystems by interfering with the central metabolic pathways of the host during infection via the expression of auxiliary metabolic genes (AMGs), altering the productivity of ecosystems and thus affecting geochemical cycling. In this study, the genetic diversity of phosphorus metabolism AMGs phoH, phoU and pstS was investigated by phylogenetic analysis, PCoA analysis, and alpha diversity analysis based on metagenomic data. It was found that the majority of the sequences were unique to Napahai plateau wetland. It was shown that the genetic diversity of phoH, phoU and pstS genes was independent of both habitats and host origins. In addition, the metabolic pathway of AMGs associated with the phosphorus cycling was identified based on metagenomic data. When phosphorus is deficient, virus utilizes AMGs to affect the metabolic pathway, contributing to higher phosphorus levels in the host and facilitating virus survival, replication, and propagation in the host cell.}, }
@article {pmid36828753, year = {2023}, author = {Mazza Rodrigues, JL and Melotto, M}, title = {Naturally engineered plant microbiomes in resource-limited ecosystems.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.02.006}, pmid = {36828753}, issn = {1878-4380}, abstract = {Nature-designed plant microbiomes may offer solutions to improve crop production and ecosystem restoration in less than optimum environments. Through a full exploration of metagenomic data, Camargo et al. showed that a previously unknown microbial diversity enhances nutrient mobilization in stress-adapted plants.}, }
@article {pmid36828645, year = {2023}, author = {Ao, Z and Xu, H and Li, M and Liu, H and Deng, M and Liu, Y}, title = {Clinical characteristics, diagnosis, outcomes and lung microbiome analysis of invasive pulmonary aspergillosis in the community-acquired pneumonia patients.}, journal = {BMJ open respiratory research}, volume = {10}, number = {1}, pages = {}, doi = {10.1136/bmjresp-2022-001358}, pmid = {36828645}, issn = {2052-4439}, abstract = {BACKGROUND: Invasive pulmonary aspergillosis (IPA) remains underestimated in patients with community-acquired pneumonia (CAP). This study aims to describe clinical features and outcomes of IPA in CAP patients, assess diagnostic performance of metagenomic next-generation sequencing (mNGS) for IPA and analyse lung microbiome via mNGS data.<br><br>METHODS: This retrospective cohort study included CAP patients from 22 April 2019 to 30 September 2021. Clinical and microbiological data were analysed. Diagnostic performance of mNGS was compared with traditional detection methods. The lung microbiome detected by mNGS was characterised and its association with clinical features was evaluated.<br><br>MAIN RESULTS: IPA was diagnosed in 26 (23.4%) of 111 CAP patients. Patients with IPA displayed depressed immunity, higher hospital mortality (30.8% vs 11.8%) and intensive care unit mortality (42.1% vs 17.5%) compared with patients without IPA. The galactomannan (GM) antigen test had the highest sensitivity (57.7%) in detecting the Aspergillus spp, followed by mNGS (42.3%), culture (30.8%) and smear (7.7%). The mNGS, culture and smear had 100% specificity, while GM test had 92.9% specificity. The microbial structure of IPA significantly differed from non-IPA patients (p<0.001; Wilcoxon test). Nineteen different species were significantly correlated with clinical outcomes and laboratory biomarkers, particularly for Streptococcus salivarius, Prevotella timonensis and Human betaherpesvirus 5.<br><br>CONCLUSIONS: Our results reveal that patients with Aspergillus infection tend to have a higher early mortality rate. The mNGS may be suggested as a complement to routine microbiological test in diagnosis of patients at risk of Aspergillus infection. The lung microbiota is associated with inflammatory, immune and metabolic conditions of IPA, and thus influences clinical outcomes.}, }
@article {pmid36828537, year = {2023}, author = {Parker, K and Wood, H and Russell, JA and Yarmosh, D and Shteyman, A and Bagnoli, J and Knight, B and Aspinwall, JR and Jacobs, J and Werking, K and Winegar, R}, title = {Development and Optimization of an Unbiased, Metagenomics-Based Pathogen Detection Workflow for Infectious Disease and Biosurveillance Applications.}, journal = {Tropical medicine and infectious disease}, volume = {8}, number = {2}, pages = {}, doi = {10.3390/tropicalmed8020121}, pmid = {36828537}, issn = {2414-6366}, abstract = {Rapid, specific, and sensitive identification of microbial pathogens is critical to infectious disease diagnosis and surveillance. Classical culture-based methods can be applied to a broad range of pathogens but have long turnaround times. Molecular methods, such as PCR, are time-effective but are not comprehensive and may not detect novel strains. Metagenomic shotgun next-generation sequencing (NGS) promises specific identification and characterization of any pathogen (viruses, bacteria, fungi, and protozoa) in a less biased way. Despite its great potential, NGS has yet to be widely adopted by clinical microbiology laboratories due in part to the absence of standardized workflows. Here, we describe a sample-to-answer workflow called PanGIA (Pan-Genomics for Infectious Agents) that includes simplified, standardized wet-lab procedures and data analysis with an easy-to-use bioinformatics tool. PanGIA is an end-to-end, multi-use workflow that can be used for pathogen detection and related applications, such as biosurveillance and biothreat detection. We performed a comprehensive survey and assessment of current, commercially available wet-lab technologies and open-source bioinformatics tools for each workflow component. The workflow includes total nucleic acid extraction from clinical human whole blood and environmental microbial forensic swabs as sample inputs, host nucleic acid depletion, dual DNA and RNA library preparation, shotgun sequencing on an Illumina MiSeq, and sequencing data analysis. The PanGIA workflow can be completed within 24 h and is currently compatible with bacteria and viruses. Here, we present data from the development and application of the clinical and environmental workflows, enabling the specific detection of pathogens associated with bloodstream infections and environmental biosurveillance, without the need for targeted assay development.}, }
@article {pmid36828358, year = {2023}, author = {Sivalingam, P and Sabatino, R and Sbaffi, T and Fontaneto, D and Corno, G and Di Cesare, A}, title = {Extracellular DNA includes an important fraction of high-risk antibiotic resistance genes in treated wastewaters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {121325}, doi = {10.1016/j.envpol.2023.121325}, pmid = {36828358}, issn = {1873-6424}, abstract = {Wastewater treatment plants are among the main hotspots for the release of antibiotic resistance genes (ARGs) into the environment. ARGs in treated wastewater can be found in the intracellular DNA (iDNA) and in the extracellular DNA (eDNA). In this study, we investigated the fate and the distribution (either in eDNA or in iDNA) of ARGs in the treated wastewaters pre and post-disinfection by shotgun metagenomics. The richness of the intracellular resistome was found to be higher than the extracellular one. However, the latter included different high risk ARGs. About 11% of the recovered metagenome assembled genomes (MAGs) from the extracted DNA was positive for at least one ARG and, among them, several were positive for more ARGs. The high-risk ARG bacA was the most frequently detected gene among the MAGs. The disinfection demonstrated to be an important driver of the composition of the antibiotic resistomes. Our results demonstrated that eDNA represents an important fraction of the overall ARGs, including a number of high-risk ARGs, which reach the environment with treated wastewater effluents. The studied disinfections only marginally affect the whole antibiotic resistome but cause important shifts from intracellular to extracellular DNA, potentially threating human health.}, }
@article {pmid36828342, year = {2023}, author = {Edridge, A and Namazi, R and Tebulo, A and Mfizi, A and Deijs, M and Koekkoek, S and de Wever, B and van der Ende, A and Umiwana, J and de Jong, MD and Jans, J and Verhoeven-Duif, N and Titulaer, M and van Karnebeek, C and Seydel, K and Taylor, T and Asiimwe-Kateera, B and van der Hoek, L and Kabayiza, JC and Mallewa, M and Idro, R and Boele van Hensbroek, M and van Woensel, JBM}, title = {Viral, bacterial, metabolic, and autoimmune causes of severe acute encephalopathy in sub-Saharan Africa: a multicenter cohort study.}, journal = {The Journal of pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jpeds.2023.02.007}, pmid = {36828342}, issn = {1097-6833}, abstract = {OBJECTIVES: To assess whether viral, bacterial, metabolic, and autoimmune diseases are missed by conventional diagnostics among children with severe acute encephalopathy in sub-Saharan Africa.<br><br>STUDY DESIGN: One hundred and thirty-four children (6m-18y) presenting with non-traumatic coma or convulsive status epilepticus to one of four medical referral centers in Uganda, Malawi and Rwanda were enrolled between 2015 and 2016. Locally available diagnostic tests could be supplemented in 117 patients by viral, bacterial and 16s quantitative polymerase chain reaction testing, metagenomics, untargeted metabolomics, and autoimmune immunohistochemistry screening.<br><br>RESULTS: Fourteen (12%) cases of viral encephalopathies, eight (7%) cases of bacterial central nervous system (CNS) infections and four (4%) cases of inherited metabolic disorders (IMDs) were newly identified by additional diagnostic testing as the most likely cause of encephalopathy. No confirmed cases of autoimmune encephalitis were found. Patients for whom additional diagnostic testing aided causal evaluation (adjusted odds ratio (AOR) 3.59, 90% confidence interval 1.57-8.36), patients with a viral CNS infection, (AOR 7.91, 90% CI 2.49-30.07) and patients with an IMD (AOR 9.10, 90% CI 1.37-110.45) were at increased risk for poor outcome of disease.<br><br>CONCLUSIONS: Viral and bacterial CNS infections and IMDs are prevalent causes of severe acute encephalopathy in children in Uganda, Malawi, and Rwanda that are missed by conventional diagnostics and are associated with poor outcome of disease. Improved diagnostic capacity may increase diagnostic yield and might improve outcome of disease.}, }
@article {pmid36827814, year = {2023}, author = {Ku, T and Liu, Y and Xie, Y and Hu, J and Hou, Y and Tan, X and Ning, X and Li, G and Sang, N}, title = {Tebuconazole mediates cognitive impairment via the microbe-gut-brain axis (MGBA) in mice.}, journal = {Environment international}, volume = {173}, number = {}, pages = {107821}, doi = {10.1016/j.envint.2023.107821}, pmid = {36827814}, issn = {1873-6750}, abstract = {Tebuconazole, one of the most widely used triazole fungicides, is reported to potentially pose a risk of inducing neurological disorders in human beings. Considering the increasing exposure, whether it could influence cognitive function remains to be elucidated. Herein, we used a mouse model to evaluate the potential cognitive risks and possible mechanisms from the continuous edible application of tebuconazole at low concentrations. Our study revealed that tebuconazole deteriorated spatial learning and memory and downregulated the expression of glutamate receptor subunits. Importantly, metagenomic analysis indicated that tebuconazole not only led to significant shifts in the composition and diversity of the gut microbiota but also changed intestinal homeostasis. Specifically, after exposure, tebuconazole circulated in the bloodstream and largely entered the gut-brain axis for disruption, including disturbing the Firmicutes/Bacteroidetes ratio, interrelated neurotransmitters and systemic immune factors. Moreover, pretreatment with probiotics improved immune factor expression and restored the deterioration of synaptic function and spatial learning and memory. The current study provides novel insights concerning perturbations of the gut microbiome and its functions as a potential new mechanism by which tebuconazole exposes cognitive function-related human health.}, }
@article {pmid36827617, year = {2023}, author = {Gabrielli, M and Dai, Z and Delafont, V and Timmers, PHA and van der Wielen, PWJJ and Antonelli, M and Pinto, AJ}, title = {Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c09010}, pmid = {36827617}, issn = {1520-5851}, abstract = {The biogeography of eukaryotes in drinking water systems is poorly understood relative to that of prokaryotes or viruses, limiting the understanding of their role and management. A challenge with studying complex eukaryotic communities is that metagenomic analysis workflows are currently not as mature as those that focus on prokaryotes or viruses. In this study, we benchmarked different strategies to recover eukaryotic sequences and genomes from metagenomic data and applied the best-performing workflow to explore the factors affecting the relative abundance and diversity of eukaryotic communities in drinking water distribution systems (DWDSs). We developed an ensemble approach exploiting k-mer- and reference-based strategies to improve eukaryotic sequence identification and identified MetaBAT2 as the best-performing binning approach for their clustering. Applying this workflow to the DWDS metagenomes showed that eukaryotic sequences typically constituted small proportions (i.e., <1%) of the overall metagenomic data with higher relative abundances in surface water-fed or chlorinated systems with high residuals. The α and β diversities of eukaryotes were correlated with those of prokaryotic and viral communities, highlighting the common role of environmental/management factors. Finally, a co-occurrence analysis highlighted clusters of eukaryotes whose members' presence and abundance in DWDSs were affected by disinfection strategies, climate conditions, and source water types.}, }
@article {pmid36827575, year = {2023}, author = {Macocco, I and Glielmo, A and Grilli, J and Laio, A}, title = {Intrinsic Dimension Estimation for Discrete Metrics.}, journal = {Physical review letters}, volume = {130}, number = {6}, pages = {067401}, doi = {10.1103/PhysRevLett.130.067401}, pmid = {36827575}, issn = {1079-7114}, abstract = {Real-world datasets characterized by discrete features are ubiquitous: from categorical surveys to clinical questionnaires, from unweighted networks to DNA sequences. Nevertheless, the most common unsupervised dimensional reduction methods are designed for continuous spaces, and their use for discrete spaces can lead to errors and biases. In this Letter we introduce an algorithm to infer the intrinsic dimension (ID) of datasets embedded in discrete spaces. We demonstrate its accuracy on benchmark datasets, and we apply it to analyze a metagenomic dataset for species fingerprinting, finding a surprisingly small ID, of order 2. This suggests that evolutive pressure acts on a low-dimensional manifold despite the high dimensionality of sequences' space.}, }
@article {pmid36827387, year = {2023}, author = {Zhao, M and Zhao, Q and Guan, Z and Liu, Q and Zhou, H and Huang, Q and Huo, B}, title = {Effect of Panax ginseng and Fructus Mume on Intestinal Barrier and Gut Microbiota in Rats with Diarrhea.}, journal = {Journal of medicinal food}, volume = {}, number = {}, pages = {}, doi = {10.1089/jmf.2022.K.0069}, pmid = {36827387}, issn = {1557-7600}, abstract = {Panax ginseng and Fructus mume (Renshen Wumei in Chinese, RW) are natural medicines with high nutritional and pharmacological value. They have been widely used together in China to treat gastrointestinal diseases, especially persistent diarrhea, but the potential mechanisms remain elusive. In this study, a diarrhea model was established in rats using a 30% aqueous extract of senna. The therapeutic effects of RW were evaluated by recording the prevalence of loose stools, the diarrhea index, and histopathological changes in colon tissue. The levels of mucins, tight junction (TJ) proteins, inflammatory cytokines, and phosphoinositide 3-kinase/Akt/nuclear factor-κB (PI3K/Akt/NF-κB) signaling pathway proteins were measured. Metagenomic sequencing was used to analyze the gut microbiota. Treatment with RW alleviated injury to the intestinal barrier in rats with diarrhea and also upregulated levels of Muc2 and TJ proteins, such as occludin, zonula occludens-1, and claudin-1. Administration of RW regulated the structure of the gut microbiota in diarrheal rats. Furthermore, RW suppressed levels of interleukin (IL), tumor necrosis factor (TNF)-α, IL-1, PI3K, Akt, and p-NF-κB p65 and also increased IL-4 levels. Our study indicates that P. ginseng and Fructus mume help improve the symptoms of diarrhea, possibly by alleviating the intestinal barrier injury, regulating intestinal flora composition, and inhibiting the PI3K/Akt/NF-κB signaling pathway.}, }
@article {pmid36827180, year = {2023}, author = {Qu, YN and Rao, YZ and Qi, YL and Li, YX and Li, A and Palmer, M and Hedlund, BP and Shu, WS and Evans, PN and Nie, GX and Hua, ZS and Li, WJ}, title = {Panguiarchaeum symbiosum, a potential hyperthermophilic symbiont in the TACK superphylum.}, journal = {Cell reports}, volume = {42}, number = {3}, pages = {112158}, doi = {10.1016/j.celrep.2023.112158}, pmid = {36827180}, issn = {2211-1247}, abstract = {The biology of Korarchaeia remains elusive due to the lack of genome representatives. Here, we reconstruct 10 closely related metagenome-assembled genomes from hot spring habitats and place them into a single species, proposed herein as Panguiarchaeum symbiosum. Functional investigation suggests that Panguiarchaeum symbiosum is strictly anaerobic and grows exclusively in thermal habitats by fermenting peptides coupled with sulfide and hydrogen production to dispose of electrons. Due to its inability to biosynthesize archaeal membranes, amino acids, and purines, this species likely exists in a symbiotic lifestyle similar to DPANN archaea. Population metagenomics and metatranscriptomic analyses demonstrated that genes associated with amino acid/peptide uptake and cell attachment exhibited positive selection and were highly expressed, supporting the proposed proteolytic catabolism and symbiotic lifestyle. Our study sheds light on the metabolism, evolution, and potential symbiotic lifestyle of Panguiarchaeum symbiosum, which may be a unique host-dependent archaeon within the TACK superphylum.}, }
@article {pmid36827117, year = {2023}, author = {Meyer, JL and Gunasekera, SP and Brown, AL and Ding, Y and Miller, S and Teplitski, M and Paul, VJ}, title = {Cryptic Diversity of Black Band Disease Cyanobacteria in Siderastrea siderea Corals Revealed by Chemical Ecology and Comparative Genome-Resolved Metagenomics.}, journal = {Marine drugs}, volume = {21}, number = {2}, pages = {}, doi = {10.3390/md21020076}, pmid = {36827117}, issn = {1660-3397}, support = {GM128742/NH/NIH HHS/United States ; }, abstract = {Black band disease is a globally distributed and easily recognizable coral disease. Despite years of study, the etiology of this coral disease, which impacts dozens of stony coral species, is not completely understood. Although black band disease mats are predominantly composed of the cyanobacterial species Roseofilum reptotaenium, other filamentous cyanobacterial strains and bacterial heterotrophs are readily detected. Through chemical ecology and metagenomic sequencing, we uncovered cryptic strains of Roseofilum species from Siderastrea siderea corals that differ from those on other corals in the Caribbean and Pacific. Isolation of metabolites from Siderastrea-derived Roseofilum revealed the prevalence of unique forms of looekeyolides, distinct from previously characterized Roseofilum reptotaenium strains. In addition, comparative genomics of Roseofilum strains showed that only Siderastrea-based Roseofilum strains have the genetic capacity to produce lasso peptides, a family of compounds with diverse biological activity. All nine Roseofilum strains examined here shared the genetic capacity to produce looekeyolides and malyngamides, suggesting these compounds support the ecology of this genus. Similar biosynthetic gene clusters are not found in other cyanobacterial genera associated with black band disease, which may suggest that looekeyolides and malyngamides contribute to disease etiology through yet unknown mechanisms.}, }
@article {pmid36827038, year = {2023}, author = {Zhang, H and Wang, X and Xia, H and Liu, Z}, title = {Metagenomics next-generation sequencing assists in the diagnosis of infant pertussis encephalopathy: A case report.}, journal = {Medicine}, volume = {102}, number = {8}, pages = {e33080}, doi = {10.1097/MD.0000000000033080}, pmid = {36827038}, issn = {1536-5964}, abstract = {RATIONALE: Pertussis is an acute respiratory infection that often occurs in the pediatric population, especially in infants under 3 months old. Bordetella pertussis is the causative agent of pertussis, which can lead to pneumonia, encephalopathy, and pulmonary hypertension, causing death in severe cases. Therefore, an accurate and comprehensive diagnosis of the pathogen is essential for effective treatment.<br><br>PATIENT CONCERNS: We report a case of 2-month-old male infant admitted to the pediatric intensive care unit of West China Second University due to hoarse cough for 7 days, accompanied by a crowing-like echo, fever and listlessness, occasional nonprojectile vomiting with anorexia, shortness of breath, accelerated heart rate, cyanosis of the lips, and convulsions. B pertussis was identified by metagenomic next-generation sequencing in blood and cerebrospinal fluid and polymerase chain reaction assay using blood.<br><br>DIAGNOSES: The infant was diagnosed with pertussis.<br><br>INTERVENTIONS: Intravenous infusion of erythromycin (50&#x2009;mg/kg/d) for anti-infection and dexamethasone for alleviating intracranial inflammatory reaction were given.<br><br>OUTCOMES: The patient was eventually recovered and discharged.<br><br>LESSONS: This case report emphasized the importance of metagenomic next-generation sequencing using cerebrospinal fluid and blood for early diagnosis of pertussis-associated encephalopathy.}, }
@article {pmid36826808, year = {2023}, author = {Tan, TC and Chandrasekaran, L and Leung, YY and Purbojati, R and Pettersson, S and Low, AHL}, title = {Gut microbiome profiling in systemic sclerosis: a metagenomic approach.}, journal = {Clinical and experimental rheumatology}, volume = {}, number = {}, pages = {}, doi = {10.55563/clinexprheumatol/jof7nx}, pmid = {36826808}, issn = {0392-856X}, abstract = {OBJECTIVES: The early gastrointestinal (GI) manifestation of systemic sclerosis (SSc) suggests a possible GI microbiota engagement in the pathophysiology and/or progression of SSc. Previous studies have revealed dysbiosis among Caucasian SSc patients. This study extends these findings in Asian SSc patients.<br><br>METHODS: Adult SSc patients, stratified according to 1) on immunosuppressive (On-IS) drugs or 2) no immunosuppressive drugs (No-IS), and age-and-sex-matched healthy controls (HC) were recruited. Metagenomic sequencing of stool DNA was compared between SSc patients and HC, and between SSc (On-IS) and (No-IS) patients. Alpha and beta-diversity, taxonomic and functional profiling were evaluated.<br><br>RESULTS: Twenty-three female SSc patients (12 On-IS; 11 No-IS; 5 diffuse and 18 limited SSc subtype) and 19 female HC, with median age of 54 years and 56 years, respectively, were recruited. Median SSc disease duration was 3.3 years. Alpha diversity was significantly higher in SSc versus HC (p=0.014) and in SSc (No-IS) versus HC (p=0.006). There was no significant difference in beta diversity between SSc and HC (p=0.307). At the phyla level, there were significantly increased abundance of Firmicutes and Actinobacteria in SSc versus HC, and reduced abundance of Bacteroidetes (all p<0.001). At the species level, there were significantly increased abundance of several Lactobacillus, Bifidobacterium, and Coprococcus species in SSc, and increased abundance of Odoribacter, Bacteroides and Prevotella species in HC. KEGG pathway analysis demonstrated distinct differences between SSc vs HC, and between SSc (No-IS) and SSc (On-IS).<br><br>CONCLUSIONS: Using metagenomic sequencing, our study further underlines distinct alterations in microbiota profiling among Asian SScpatients.}, }
@article {pmid36826766, year = {2023}, author = {Ji, B and Qin, J and Ma, Y and Liu, X and Wang, T and Liu, G and Li, B and Wang, G and Gao, P}, title = {Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {36826766}, issn = {1614-7499}, abstract = {In actual production environments, antibiotic-resistant genes (ARGs) are abundant in pig manure, which can form transmission chains through animals, the environment, and humans, thereby threatening human health. Therefore, based on metagenomic analysis methods, ARGs and mobile genetic elements (MGEs) were annotated in pig manure samples from 6 pig farms in 3 regions of Shanxi Province, and the potential hosts of ARGs were analyzed. The results showed that a total of 14 ARG types were detected, including 182 ARG subtypes, among which tetracycline, phenol, aminoglycoside, and macrolide resistance genes were the main ones. ARG profiles, MGE composition, and microbial communities were significantly different in different regions as well as between different pig farms. In addition, Anaerobutyricum, Butyrivibrio, and Turicibacter were significantly associated with multiple ARGs, and bacteria such as Prevotella, Bacteroides, and the family Oscillospiraceae carried multiple ARGs, suggesting that these bacteria are potential ARG hosts in pig manure. Procrustes analysis showed that bacterial communities and MGEs were significantly correlated with ARG profiles. Variation partitioning analysis results indicated that the combined effect of MGEs and bacterial communities accounted for 64.08% of resistance variation and played an important role in ARG profiles. These findings contribute to our understanding of the dissemination and persistence of ARGs in actual production settings, and offer some guidance for the prevention and control of ARGs contamination.}, }
@article {pmid36825940, year = {2023}, author = {Almas, S and Carpenter, RE and Singh, A and Rowan, C and Tamrakar, VK and Sharma, R}, title = {Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential.}, journal = {Advances in respiratory medicine}, volume = {91}, number = {1}, pages = {49-65}, doi = {10.3390/arm91010006}, pmid = {36825940}, issn = {2543-6031}, abstract = {Although it is clinically important for acute respiratory tract (co)infections to have a rapid and accurate diagnosis, it is critical that respiratory medicine understands the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n = 29) with a commercially available PCR assay and compared the results with those of a hybridization-capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct < 35 and for mNGS samples it was >40% target coverage, median depth of 1X and RPKM > 10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positively 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterized the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify[®] Platform (Illumina[®] Inc, San Diego, CA, USA) for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompromised or immunocompetent with comorbidity respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndrome-based tests, and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration-with promise to reduce morbidity and mortality.}, }
@article {pmid36825821, year = {2023}, author = {Gautam, A and Zeng, W and Huson, DH}, title = {MeganServer: facilitating interactive access to metagenomic data on a server.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btad105}, pmid = {36825821}, issn = {1367-4811}, abstract = {MOTIVATION: Metagenomic projects often involve large numbers of large sequencing datasets (totaling hundreds of gigabytes of data). Thus, computational preprocessing and analysis are usually performed on a server. The results of such analyses are then usually explored interactively. One approach is to use MEGAN, an interactive program that allows analysis and comparison of metagenomic datasets. Previous releases have required that the user first download the computed data from the server, an increasingly time-consuming process. Here we present MeganServer, a stand-alone program that serves MEGAN files to the web, using a RESTful API, facilitating interactive analysis in MEGAN, without requiring prior download of the data. We describe a number of different application scenarios.<br><br>AVAILABILITY: MeganServer is provided as a standalone program tools/megan-server in the MEGAN software suite, available at https://software-ab.cs.uni-tuebingen.de/download/megan6. Source available at: https://github.com/husonlab/megan-ce/tree/master/src/megan/ms.<br><br>SUPPLEMENTARY INFORMATION: A description of how to get started is available at Bioinformatics online.}, }
@article {pmid36825261, year = {2022}, author = {Ohkusa, T and Nishikawa, Y and Sato, N}, title = {Gastrointestinal disorders and intestinal bacteria: Advances in research and applications in therapy.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {935676}, doi = {10.3389/fmed.2022.935676}, pmid = {36825261}, issn = {2296-858X}, abstract = {Intestinal bacteria coexist with humans and play a role in suppressing the invasion of pathogens, producing short-chain fatty acids, producing vitamins, and controlling the immune system. Studies have been carried out on culturable bacterial species using bacterial culture methods for many years. However, as metagenomic analysis of bacterial genes has been developed since the 1990s, it has recently revealed that many bacteria in the intestine cannot be cultured and that approximately 1,000 species and 40 trillion bacteria are present in the gut microbiota. Furthermore, the composition of the microbiota is different in each disease state compared with the healthy state, and dysbiosis has received much attention as a cause of various diseases. Regarding gastrointestinal diseases, dysbiosis has been reported to be involved in inflammatory bowel disease, irritable bowel syndrome, and non-alcoholic steatohepatitis. Recent findings have also suggested that dysbiosis is involved in colon cancer, liver cancer, pancreatic cancer, esophageal cancer, and so on. This review focuses on the relationship between the gut microbiota and gastrointestinal/hepatobiliary diseases and also discusses new therapies targeting the gut microbiota.}, }
@article {pmid36825092, year = {2023}, author = {Liu, H and Xu, J and Yeung, C and Chen, Q and Li, J}, title = {Effects of hemicellulose on intestinal mucosal barrier integrity, gut microbiota, and metabolomics in a mouse model of type 2 diabetes mellitus.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1096471}, doi = {10.3389/fmicb.2023.1096471}, pmid = {36825092}, issn = {1664-302X}, abstract = {BACKGROUND AND OBJECTIVE: Impaired gut barrier contributes to the progression of type 2 diabetes mellitus (T2DM), and the gut microbiota and metabolome play an important role in it. Hemicellulose, a potential prebiotics, how its supplementation impacted the glucose level, the impaired gut barrier, and the gut microbiota and metabolome in T2DM remained unclear.<br><br>METHODS: In this study, some mice were arranged randomly into four groups: db/db mice fed by a compositionally defined diet (CDD), db/db mice fed by a CDD with 10% and 20% hemicellulose supplementation, and control mice fed by a CDD. Body weight and fasting blood glucose levels were monitored weekly. The gut barrier was evaluated. Fresh stool samples were analyzed using metagenomic sequencing and liquid chromatography-mass spectrometry to detect gut microbiota and metabolome changes. Systemic and colonic inflammation were evaluated.<br><br>RESULTS: Better glycemic control, restoration of the impaired gut barrier, and lowered systemic inflammation levels were observed in db/db mice with the supplementation of 10 or 20% hemicellulose. The gut microbiota showed significant differences in beta diversity among the four groups. Fifteen genera with differential relative abundances and 59 significantly different metabolites were found. In the db/db group, hemicellulose eliminated the redundant Faecalibaculum and Enterorhabdus. The increased succinate and ursodeoxycholic acid (UDCA) after hemicellulose treatment were negatively correlated with Bifidobacterium, Erysipelatoclostridium, and Faecalibaculum. In addition, hemicellulose reduced the colonic expressions of TLR2/4 and TNF-&#x3b1; in db/db mice.<br><br>CONCLUSION: Hemicellulose may serve as a potential therapeutic intervention for T2DM by improving impaired intestinal mucosal barrier integrity, modulating gut microbiota composition, and altering the metabolic profile.}, }
@article {pmid36824891, year = {2023}, author = {Pastar, I and Dinic, M and Verpile, R and Meng, J and Marjanovic, J and Burgess, J and Plano, L and Hower, S and Thaller, S and Banerjee, S and Lev-Tov, H and Tomic-Canic, M}, title = {Chronic wound microenvironment mediates selection of biofilm-forming multi drug resistant Staphylococcus epidermidis with capability to impair healing.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-2562300/v1}, pmid = {36824891}, abstract = {Venous leg ulcers (VLU) are the most common chronic wounds characterized by bacterial biofilms and perturbed microbiome. Staphylococcus epidermidis is primarily known as skin commensal beneficial for the host, however, some strains can form biofilms and cause infections. By employing shotgun metagenomic sequencing we show that genetic signatures of antimicrobial resistance, adhesion and biofilm formation in VLU isolates correlate with in vitro bacterial traits. We demonstrate that the capability of chronic wound isolates to form biofilms and elicit IL-8 and IL-1β expression in human ex vivo wounds, correlates with the non-healing outcomes in patients with VLU. In contrast, commensal strains were incapable of surviving in the human ex vivo wounds. We show that major fitness traits of S. epidermis from VLU involve genes for resistance to methicillin and mupirocin, while the biofilm formation relied on the minimal number of genetic elements responsible for bacterial binding to fibronectin and fibrinogen. This underscores the importance of the emergence of treatment resistant virulent lineages in patients with non-healing wounds.}, }
@article {pmid36824686, year = {2023}, author = {Shen, M and Li, Q and Zeng, Z and Han, D and Luo, X}, title = {Mucor indicus caused disseminated infection diagnosed by metagenomic next-generation sequencing in an acute myeloid leukemia patient: A case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1089196}, doi = {10.3389/fcimb.2023.1089196}, pmid = {36824686}, issn = {2235-2988}, abstract = {BACKGROUND: Mucormycosis commonly occurs in immunosuppressed patients with hematological diseases, which can be life-threatening. However, many cases are often misdiagnosed due to lack of specific clinical manifestations. Additionally, the traditional blood culture or serological testing, with a high false-negative rate, is time-consuming. Thus, precise and timely diagnosis of infections is essential for the clinical care of infected patients.<br><br>CASE PRESENTATION: We report a 29-year-old Chinese man with acute myeloid leukemia (AML) who developed febrile neutropenia after the first course of induction chemotherapy. He received empirical antibiotics, which did not relieve his symptoms. No pathogen was detected by traditional microbiologic assays, while Mucor indicus was identified by metagenomic next-generation sequencing (mNGS) in the blood specimen. Liposomal amphotericin B (LAmB) was used, resulting in the patient's temperature returning to normal. A few days later, abdominal computed tomography (CT) scan showed multiple liver abscesses; fluorescence staining, histopathology, and mNGS identified the causative agent-M. indicus. Posaconazole was combined with LAmB as long-term antifungal treatment. Finally, the patient received allogeneic hematopoietic stem cell transplantation successfully after controlled infection. During follow-up 1 year after transplantation, the number of liver abscesses was reduced to one and remained stable.<br><br>CONCLUSION: This report described the first case of an AML patient diagnosed with culture-negative disseminated infections caused by M. indicus leading to rare hepatic manifestations using mNGS of peripheral blood and liver biopsy. LAmB combined with posaconazole was given in time, resulting in a favorable outcome. mNGS is a new method that assists in detecting the probable pathogen and increases the accuracy of identifying an etiology.}, }
@article {pmid36824263, year = {2023}, author = {Sheng, S and Li, X and Zhao, S and Zheng, C and Zhang, F}, title = {Effects of levodopa on gut bacterial antibiotic resistance in Parkinson's disease rat.}, journal = {Frontiers in aging neuroscience}, volume = {15}, number = {}, pages = {1122712}, doi = {10.3389/fnagi.2023.1122712}, pmid = {36824263}, issn = {1663-4365}, abstract = {The second most prevalent neurodegenerative ailment, Parkinson's disease (PD), is characterized by both motor and non-motor symptoms. Levodopa is the backbone of treatment for PD at the moment. However, levodopa-induced side effects, such as dyskinesia, are commonly seen in PD patients. Recently, several antibiotics were fo