@article {pmid34871697,
year = {2021},
author = {Tong, C and Xiao, D and Xie, L and Yang, J and Zhao, R and Hao, J and Huo, Z and Zeng, Z and Xiong, W},
title = {Swine manure facilitates the spread of antibiotic resistome including tigecycline-resistant tet(X) variants to farm workers and receiving environment.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {152157},
doi = {10.1016/j.scitotenv.2021.152157},
pmid = {34871697},
issn = {1879-1026},
abstract = {The prevalence of antibiotic resistance genes (ARGs) in livestock and poultry manure is a severe threat to human health. However, the comprehensive characterization of antibiotic resistance in swine, workers, and the receiving environment is still lacking in the actual breeding environment. Hence, the ARG profile and the potential bacterial hosts producing among swine manure (including sows, piglets, finishing pigs, and nursery pigs), worker feces, and the receiving environment (including sediment and vegetable soil) were comprehensively analyzed based on the metagenomic method. The results showed that swine manure exhibited the high levels of richness and diversity of ARGs. Inactivating tetracycline resistance genes such as tet(X), tet(X1), and tet(X10) were prevalent on swine farms. Workers and the environment were the primary recipients of ARGs, and shared ARGs accounted for at least 90% of their ARG abundances. Network analysis revealed that Escherichia, Acinetobacter, and Erysipelothrix were the most dominant genera co-occurring with specific shared ARGs. The abundance of coexisting ARGs in swine at different developmental stages accounted for 76.4% to 90.8% of the shared ARGs in swine, workers, and environmental samples. The Mantel test revealed that Firmicutes and Proteobacteria had a significant correlation with the ARG profiles. In addition, variation partitioning analysis (VPA) showed that the joint effects of mobile genetic elements (MGEs) and bacterial communities accounted for 24.7% of the resistome variation and played a significant role in the ARG profiles. These results improve our understanding of the transmission and persistence of ARGs in the actual breeding environment.},
}

@article {pmid34871608,
year = {2021},
author = {Liu, Y and Wang, Q and Pan, Q and Zhou, X and Peng, Z and Jahng, D and Yang, B and Pan, X},
title = {Ventilation induced evolution pattern of archaea, fungi, bacteria and their potential roles during co-bioevaporation treatment of concentrated landfill leachate and food waste.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {133122},
doi = {10.1016/j.chemosphere.2021.133122},
pmid = {34871608},
issn = {1879-1298},
abstract = {To obtain a favorable aeration type in co-bioevaporation treatment of concentrated landfill leachate and food waste, and to deeply understand the co-bioevaporation mechanisms, the temporal evolution differences of archaea, fungi and bacteria as well as the related microbial metabolism genes and functional enzymes under intermittent ventilation (IV) and continuous ventilation (CV) were investigated. Results through metagenomics analysis showed that the less sufficient oxygen and longer thermophilic phase in IV stimulated the vigorous growth of archaea, while CV was beneficial for fungal growth. Even genes of carbohydrates and lipids metabolism and ATP-associated enzymes (enzyme 2.7.13.3 and 3.6.4.12), as well as peptidoglycan biosynthesis enzyme (enzyme 3.4.16.4), were more abundant in CV, IV hold better DNA repair ability, higher microbial viability, and less dehydrogenase sensitivity to temperatures due to the critical contribution of Pseudomonas (3.1-45.9%). Furthermore, IV consumed a similar amount of heat for water evaporation with nearly half of the ventilation of CV and was a favorable aeration type in the practical application of co-bioevaporation.},
}

@article {pmid34871595,
year = {2021},
author = {Liu, X and Tang, R and Li, H and Wang, L and Wan, C},
title = {The physiological and ecological properties of bacterial persisters discovered from municipal sewage sludge and the potential risk.},
journal = {Environmental research},
volume = {},
number = {},
pages = {112481},
doi = {10.1016/j.envres.2021.112481},
pmid = {34871595},
issn = {1096-0953},
abstract = {Bacterial persisters are a special microbial population and are considered to be the bacterial reservoir of antibiotic-resistant bacteria. They can survive antibiotic treatment even in high concentrations of antibiotics and revive in the appropriate conditions. However, the characteristics of bacterial persisters in the municipal sewage sludge and their potential environmental risks have not yet been paid much attention to. In this study, bacterial persisters were discovered from the sludge of wastewater treatment plants in four different regions (Jilin, Lhasa, Shenzhen, and Yili), and the metagenomic analysis confirmed that bacterial persisters were ubiquitous in all four municipal sewage sludge and positively related to the protobacterium populations. At the taxonomic genus level, a total of 57 genera of bacterial persisters were shared by the four sewage sludge, and the genera with abundance exceeding 2% were Acinetobacter, Lysinibacillus, Aeromonas, Brevundimonas, Pseudomonas, and Alcaligenes, among which Acinetobacter accounted for 57.24%. Genus Lysinibacillus and Aeromonas were significant in Jilin and Lhasa, respectively. The persistence mechanism of bacterial persisters derived from sludge was also clarified, among which, Aeromonas, Brevundimonas, and Alcaligenes rely on the hipBA toxin-antitoxin system, while Acinetobacter enters the persistence state mainly through the stringent response system based on (p)ppGpp. Moreover, it was found that a typical bacterial persister originated from Acinetobacter, named T9-9, could tolerate a variety of antibiotics, such as 1000 μg/mL of kanamycin, 160 μg/mL of tetracycline, and 30 μg/mL of ciprofloxacin. Even if the ultraviolet intensity was 6-36 times the usual dosage of ultraviolet disinfection in wastewater treatment plants, it could not completely kill T9-9, but the killing efficiency by chlorine disinfection technology could reach 100%. This study pointed out an environmental risk of bacterial persisters that existed in sewage sludge that had been neglected and strongly recommended to improve the disinfection process in the wastewater treatment plant.},
}

@article {pmid34870848,
year = {2021},
author = {Chen, J and Li, Y and Jing, H and Zhang, X and Xu, Z and Xu, J and Liu, H},
title = {Genomic and transcriptomic evidence for the diverse adaptations of subclusters 5.2 and 5.3 Synechococcus to mesoscale eddies.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.17903},
pmid = {34870848},
issn = {1469-8137},
abstract = {Mesoscale eddies are ubiquitous oceanographic features that influence the metabolism and community structure of Synechococcus. However, the metabolic adaptations of this genus to eddy-associated environmental changes have rarely been studied. We recovered two high-quality Synechococcus metagenome-assembled genomes (MAGs) from eddies in the South China Sea and compared their metabolic variations using metatranscriptomic samples obtained at the same time. The two MAGs (syn-bin1 and syn-bin2) are affiliated with marine Synechococcus subclusters 5.2 (S5.2) and 5.3 (S5.3), respectively. The former exhibited a higher abundance at the surface layer, whereas the latter was more abundant in deep euphotic layer. Further analysis indicated that syn-bin1 had a strong capability to utilize organic nutrients, which could help it to thrive in the nutrient-deprived surface water. In contrast, syn-bin2 had the genetic potential to perform chromatic acclimation, which could allow it to capture green or blue light at different depths. Additionally, transcriptomic analysis showed that syn-bin2 upregulated genes involved in the synthesis of C4 acids, photosystem II proteins, and HCO3 - transporters in deep euphotic layer, which might contribute to its predominance in low-light environment. Overall, this study extends our understanding of oceanic S5.2 and S5.3 Synechococcus by revealing their metabolic adaptations to mesoscale eddies.},
}

@article {pmid34870622,
year = {2022},
author = {Redd, TK and Lalitha, P and Prajna, NV and Sikha, M and Gunasekaran, R and Hinterwirth, A and Chen, C and Zhong, L and Liu, Z and Lietman, TM and Keenan, JD and Doan, T and Seitzman, GD},
title = {Impact of Sample Collection Order on the Diagnostic Performance of Metagenomic Deep Sequencing for Infectious Keratitis.},
journal = {Cornea},
volume = {41},
number = {1},
pages = {39-44},
doi = {10.1097/ICO.0000000000002766},
pmid = {34870622},
issn = {1536-4798},
abstract = {PURPOSE: The purpose of this article was to evaluate the impact of sample collection order on the diagnostic yield of metagenomic deep sequencing (MDS) for determining the causative pathogen in infectious keratitis.

METHODS: We performed a cross-sectional diagnostic test evaluation among subjects with infectious keratitis at Aravind Eye Hospital in Madurai, India. All subjects underwent corneal scrapings of the affected eye to obtain potassium hydroxide smear, Gram stain, bacterial culture, and fungal culture, in this order. The order of MDS specimen collection relative to smear and culture samples was randomized and served as the primary predictor. Outcomes included the normalized copy number of pathogenic RNA detected by MDS, the proportion of MDS samples that were diagnostic, and the agreement of MDS results with cultures.

RESULTS: MDS samples from 46 subjects with corneal ulcers were evaluated. MDS was positive in 33 subjects (76%) and had 74% overall agreement with culture results. There was no association between order of MDS sample collection and normalized copy number of genetic material detected (P = 0.62) or the likelihood of MDS positivity (P = 0.46). However, the likelihood of agreement between MDS and cultures decreased when MDS corneal swabs were collected after other diagnostic corneal scrapings (P = 0.05).

CONCLUSIONS: The overall yield of MDS for detecting the cause of infectious keratitis was not affected by sample collection order. However, diagnostic agreement between MDS and cultures decreased when MDS samples were collected after other specimens. Additional investigation is warranted to determine whether this represents increased sensitivity of MDS compared with cultures or higher susceptibility to contaminants.},
}

@article {pmid34869767,
year = {2021},
author = {Yu, X and Jiang, W and Huang, X and Lin, J and Ye, H and Liu, B},
title = {rRNA Analysis Based on Long-Read High-Throughput Sequencing Reveals a More Accurate Diagnostic for the Bacterial Infection of Ascites.},
journal = {BioMed research international},
volume = {2021},
number = {},
pages = {6287280},
doi = {10.1155/2021/6287280},
pmid = {34869767},
issn = {2314-6141},
abstract = {Traditional pathogenic diagnosis presents defects such as a low positivity rate, inability to identify uncultured microorganisms, and time-consuming nature. Clinical metagenomics next-generation sequencing can be used to detect any pathogen, compensating for the shortcomings of traditional pathogenic diagnosis. We report third-generation long-read sequencing results and second-generation short-read sequencing results for ascitic fluid from a patient with liver ascites and compared the two types of sequencing results with the results of traditional clinical microbial culture. The distribution of pathogenic microbial species revealed by the two types of sequencing results was quite different, and the third-generation sequencing results were consistent with the results of traditional microbial culture, which can effectively guide subsequent treatment. Short reads, the lack of amplification, and enrichment to amplify signals from trace pathogens, and host background noise may be the reasons for the high error in the second-generation short-read sequencing results. Therefore, we propose that long-read-based rRNA analysis technology is superior to the short-read shotgun-based metagenomics method in the identification of pathogenic bacteria.},
}

@article {pmid34869737,
year = {2021},
author = {Ning, S and Lu, X and Zhao, M and Wang, X and Yang, S and Shen, Q and Wang, H and Zhang, W},
title = {Virome in Fecal Samples From Wild Giant Pandas (Ailuropoda Melanoleuca).},
journal = {Frontiers in veterinary science},
volume = {8},
number = {},
pages = {767494},
doi = {10.3389/fvets.2021.767494},
pmid = {34869737},
issn = {2297-1769},
abstract = {The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals in the world; anthropogenic habitat loss and poaching still threaten the survival of wild pandas. Viral infection has become one of the potential threats to the health of these animals, but the available information related to these infections is still limited. In order to detect possible vertebrate viruses, the virome in the fecal samples of seven wild giant pandas from Qinling Mountains was investigated by using the method of viral metagenomics. From the fecal virome of wild giant pandas, we determined six nearly complete genomes belonging to the order Picornavirales, two of which may be qualified as a novel virus family or genus. In addition, four complete genomes belonging to the Genomoviridae family were also fully characterized. This virological investigation has increased our understanding of the gut viral community in giant pandas. Whether these viruses detected in fecal samples can really infect giant panda needs further research.},
}

@article {pmid34869453,
year = {2021},
author = {Sun, L and Li, P and Pang, B and Wu, P and Wang, R},
title = {Gestational Psittacosis With Secondary Hemophagocytic Syndrome: A Case Report and Literature Review.},
journal = {Frontiers in medicine},
volume = {8},
number = {},
pages = {755669},
doi = {10.3389/fmed.2021.755669},
pmid = {34869453},
issn = {2296-858X},
abstract = {Gestational psittacosis and hemophagocytic syndrome (HPS) are rare clinical diseases. In this article, a case of gestational psittacosis concomitant with secondary HPS was reported. An analysis was performed on the clinical characteristics, signs, laboratory findings, progression, diagnosis, and treatment of a patient with gestational psittacosis concomitant with secondary HPS. Besides, the literature with respect to this disease was reviewed. This patient was definitively diagnosed through metagenomic next-generation sequencing techniques, bone marrow puncture and smear examination, and the determination of sCD25 level and natural killer (NK) cell activity. Anti-infectives such as doxycycline and etoposide combined with hormone chemotherapy achieved significant improvement in cough and expectoration, a return to normal temperature, and a significant improvement in oxygenation index. In addition, chest computed tomography revealed obvious absorption of lung lesions and a return of NK cell activity and sCD25 levels to normal ranges. Chlamydia psittaci pneumonia requires a clear determination of etiology, while HPS requires bone marrow puncture and smear examination, together with the determination of sCD25 level and NK cell activity in the blood. The findings of this study suggest that metagenomic next-generation sequencing is an effective instrument in clearly identifying pathogens that cause lung infection. Clinicians should consider atypical pathogens of lung infection in patients with poor response to empirical anti-infectives, and strive to design an effective treatment strategy as per an accurate diagnosis based on the etiology. As for patients suffering from long-term high fever and poor temperature control after broad-spectrum antibiotic treatment, non-infectious fever should be taken into account. A rapid and clear diagnosis would significantly improve patient prognosis.},
}

@article {pmid34869420,
year = {2021},
author = {Arunasri, K and Sai Prashanthi, G and Tyagi, M and Pappuru, RR and Shivaji, S},
title = {Intraocular Viral Communities Associated With Post-fever Retinitis.},
journal = {Frontiers in medicine},
volume = {8},
number = {},
pages = {724195},
doi = {10.3389/fmed.2021.724195},
pmid = {34869420},
issn = {2296-858X},
abstract = {The virome of ocular fluids is naive. The results of this study highlight the virome in the vitreous fluid of the eye of individuals without any ocular infection and compare it with the virome of the vitreous fluid of individuals with retinitis. A total of 1,016,037 viral reads were generated from 25 vitreous fluid samples comprising control and post-fever retinitis (PFR) samples. The top 10 viral families in the vitreous fluids comprised of Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae, Poxviridae, Iridoviridae, Podoviridae, Retroviridae, Baculoviridae, and Flaviviridae. Principal coordinate analysis and heat map analysis clearly discriminated the virome of the vitreous fluid of the controls from that of the PFR virome. The abundance of 10 viral genera increased significantly in the vitreous fluid virome of the post-fever retinitis group compared with the control group. Genus Lymphocryptovirus, comprising the human pathogen Epstein-Barr virus (EBV) that is also implicated in ocular infections was significantly abundant in eight out of the nine vitreous fluid viromes of post-fever retinitis group samples compared with the control viromes. Human viruses, such as Hepacivirus, Circovirus, and Kobuvirus, were also significantly increased in abundance in the vitreous fluid viromes of post-fever retinitis group samples compared with the control viromes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analysis and the network analysis depicted an increase in the immune response by the host in the post-fever retinitis group compared with the control group. All together, the results of the study indicate changes in the virome in the vitreous fluid of patients with the post-fever retinitis group compared to the control group.},
}

@article {pmid34869341,
year = {2021},
author = {Qin, Q and Yan, S and Yang, Y and Chen, J and Yan, H and Li, T and Gao, X and Wang, Y and Li, A and Wang, S and Ding, S},
title = {The Relationship Between Osteoporosis and Intestinal Microbes in the Henan Province of China.},
journal = {Frontiers in cell and developmental biology},
volume = {9},
number = {},
pages = {752990},
doi = {10.3389/fcell.2021.752990},
pmid = {34869341},
issn = {2296-634X},
abstract = {Osteoporosis (OP) is a chronic disease in the elderly, and China is entering an aging demographic trend. In recent years, increasing evidence has demonstrated that probiotics can treat osteoporosis. This study aimed to explore the relevant mechanisms and to validate the beneficial effect on osteoporosis by high-throughput metagenome-wide gene sequencing in humans. In this study, compared with controls, several species had altered abundances, and specific functional pathways were found in the OP group. At the species level, the species that had increased in OP individuals were positively correlated to bone resorption markers and negatively correlated to 25-OH-D3 and bone formation markers, with Streptococcus sanguinis showing the strongest relevance, followed by Streptococcus gordonii, Actinomyces odontolyticus, and Olsenella unclassified. Additionally, Actinomyces graevenitzii, enriched in the OP group, was positively correlated to inflammation indicators that included white blood cell (WBC), neutrophil count (NEC), and the neutrophil-to-lymphocyte ratio (NLR) (p < 0.05). Conversely, the levels of Akkermansia muciniphila, Bacteroides eggerthii, Bacteroides fragilis, Bacteroides uniformis, and Butyricimonas synergistic were increased in the control group, which had a negative correlation with bone resorption markers and positive correlation with bone formation markers and 25-OH-D3. Additionally, Bacteroides fragilis had a negative correlation with inflammation indicators (WBC, NEC, and NLR) and the above pathways (p < 0.05). Functional prediction revealed that 106 metabolic pathways, enriched in the OP group, were significantly higher than in the control group (p < 0.05). In particular, pathways related to LPS biosynthesis, phytate degradation, lactate acid, and ethanol fermentation were more abundant in the OP group than in the control and were positively related to WBC and NEC. Taken together, several species with altered abundances and specific functional pathways were found in OP individuals. The role of phytases in OP provides novel epidemiological evidence to elucidate the underlying microbiota-relevant mechanisms in bone mineralization and should be explored further.},
}

@article {pmid34869308,
year = {2021},
author = {Pratt, M and Forbes, JD and Knox, NC and Bernstein, CN and Van Domselaar, G},
title = {Microbiome-Mediated Immune Signaling in Inflammatory Bowel Disease and Colorectal Cancer: Support From Meta-omics Data.},
journal = {Frontiers in cell and developmental biology},
volume = {9},
number = {},
pages = {716604},
doi = {10.3389/fcell.2021.716604},
pmid = {34869308},
issn = {2296-634X},
abstract = {Chronic intestinal inflammation and microbial dysbiosis are hallmarks of colorectal cancer (CRC) and inflammatory bowel diseases (IBD), such as Crohn's disease and ulcerative colitis. However, the mechanistic relationship between gut dysbiosis and disease has not yet been fully characterized. Although the "trigger" of intestinal inflammation remains unknown, a wealth of evidence supports the role of the gut microbiome as a mutualistic pseudo-organ that significantly influences intestinal homeostasis and is capable of regulating host immunity. In recent years, culture-independent methods for assessing microbial communities as a whole (termed meta-omics) have grown beyond taxonomic identification and genome characterization (metagenomics) into new fields of research that collectively expand our knowledge of microbiomes. Metatranscriptomics, metaproteomics, and metabolomics are meta-omics techniques that aim to describe and quantify the functional activity of the gut microbiome. Uncovering microbial metabolic contributions in the context of IBD and CRC using these approaches provides insight into how the metabolic microenvironment of the GI tract shapes microbial community structure and how the microbiome, in turn, influences the surrounding ecosystem. Immunological studies in germ-free and wild-type mice have described several host-microbiome interactions that may play a role in autoinflammation. Chronic colitis is a precursor to CRC, and changes in the gut microbiome may be an important link triggering the neoplastic process in chronic colitis. In this review, we describe several microbiome-mediated mechanisms of host immune signaling, such as short-chain fatty acid (SCFA) and bile acid metabolism, inflammasome activation, and cytokine regulation in the context of IBD and CRC, and discuss the supporting role for these mechanisms by meta-omics data.},
}

@article {pmid34867879,
year = {2021},
author = {Chu, C and Fan, M and Song, C and Li, N and Zhang, C and Fu, S and Wang, W and Yang, Z},
title = {Unveiling Endophytic Bacterial Community Structures of Different Rice Cultivars Grown in a Cadmium-Contaminated Paddy Field.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {756327},
doi = {10.3389/fmicb.2021.756327},
pmid = {34867879},
issn = {1664-302X},
abstract = {Endophytic bacteria play potentially important roles in the processes of plant adaptation to the environment. Understanding the composition and dynamics of endophytic bacterial communities under heavy metal (HM) stress can reveal their impacts on host development and stress tolerance. In this study, we investigated root endophytic bacterial communities of different rice cultivars grown in a cadmium (Cd)-contaminated paddy field. These rice cultivars are classified into low (RBQ, 728B, and NX1B) and high (BB and S95B) levels of Cd-accumulating capacity. Our metagenomic analysis targeting 16S rRNA gene sequence data reveals that Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes, and Spirochaetes are predominant root endophytic bacterial phyla of the five rice cultivars that we studied. Principal coordinate analysis shows that the developmental stage of rice governs a larger source of variation in the bacterial communities compared to that of any specific rice cultivar or of the root Cd content. Endophytic bacterial communities during the reproductive stage of rice form a more highly interconnected network and exhibit higher operational taxonomic unit numbers, diversities, and abundance than those during the vegetative stage. Forty-five genera are significantly correlated with Cd content in rice root, notably including positive-correlating Geobacter and Haliangium; and negative-correlating Pseudomonas and Streptacidiphilus. Furthermore, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis shows that functional pathways, such as biosynthesis of siderophore and type II polyketide products, are significantly enhanced during the reproductive stage compared to those during the vegetative stage under Cd stress. The isolated endophytic bacteria from the Cd-contaminated rice roots display high Cd resistance and multiple traits that may promote plant growth, suggesting their potential application in alleviating HM stress on plants. This study describes in detail for the first time the assemblage of the bacterial endophytomes of rice roots under Cd stress and may provide insights into the interactions among endophytes, plants, and HM contamination.},
}

@article {pmid34867874,
year = {2021},
author = {Oulas, A and Zachariou, M and Chasapis, CT and Tomazou, M and Ijaz, UZ and Schmartz, GP and Spyrou, GM and Vlamis-Gardikas, A},
title = {Putative Antimicrobial Peptides Within Bacterial Proteomes Affect Bacterial Predominance: A Network Analysis Perspective.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {752674},
doi = {10.3389/fmicb.2021.752674},
pmid = {34867874},
issn = {1664-302X},
abstract = {The predominance of bacterial taxa in the gut, was examined in view of the putative antimicrobial peptide sequences (AMPs) within their proteomes. The working assumption was that compatible bacteria would share homology and thus immunity to their putative AMPs, while competing taxa would have dissimilarities in their proteome-hidden AMPs. A network-based method ("Bacterial Wars") was developed to handle sequence similarities of predicted AMPs among UniProt-derived protein sequences from different bacterial taxa, while a resulting parameter ("Die" score) suggested which taxa would prevail in a defined microbiome. T he working hypothesis was examined by correlating the calculated Die scores, to the abundance of bacterial taxa from gut microbiomes from different states of health and disease. Eleven publicly available 16S rRNA datasets and a dataset from a full shotgun metagenomics served for the analysis. The overall conclusion was that AMPs encrypted within bacterial proteomes affected the predominance of bacterial taxa in chemospheres.},
}

@article {pmid34867862,
year = {2021},
author = {Liu, G and Li, P and Hou, L and Niu, Q and Pu, G and Wang, B and Du, T and Kim, SW and Niu, P and Li, Q and Huang, R},
title = {Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {746717},
doi = {10.3389/fmicb.2021.746717},
pmid = {34867862},
issn = {1664-302X},
abstract = {Making full use of high fiber and low-cost crop coproducts is helpful to alleviate the situation of people and livestock competing for crops. Digestion of dietary fibers in pigs is mainly through microbial fermentation in the large intestine. To reveal microbiota related to fiber digestion in pigs, fecal samples have been collected from 274 healthy female Suhuai pigs at 160 days of age under the same feeding conditions and have measured apparent neutral detergent fiber (NDF) and acid detergent fiber (ADF) digestibility. Samples from Suhuai pigs with extreme high and low apparent NDF digestibility and extreme high and low apparent ADF digestibility were subjected to shotgun metagenomic sequencing. At the species level, 62 microbial species in H_NDF group and 54 microbial species in H_ADF group were related to high fiber digestibility. Among them, Lachnospiraceae bacterium 3-1 and Alistipes sp. CAG:514 may be new types of microorganisms associated with fiber digestion. In addition, we found that more abundant GH5 and GH48 family (contribute to cellulose degradation) genes, GH39 and GH53 family (contribute to hemicellulose degradation) genes in microorganisms may contribute to the higher apparent NDF digestibility of pigs, and more abundant GH3 and GH9 family (contribute to cellulose degradation) genes in microorganisms may contribute to the higher apparent ADF digestibility of pigs. The abundance of AA4 family (helps in lignin degradation) genes in H_NDF and H_ADF groups was significantly higher than that in L_NDF and L_ADF groups, respectively (P < 0.05). Three pathways in H_NDF group and four pathways in H_ADF group are important pathways associated with degradation of non-starch polysaccharides, and their relative abundance is significantly higher than that in L_NDF and L_ADF groups, respectively. Gut microbiota of Suhuai pigs with high apparent fiber digestibility had higher abundance of genes and microbiota related to fiber digestion and may have stronger fiber digestion potential compared with low apparent fiber digestibility group. This study revealed that the characteristics of gut microbiota and microbial gene functions of pigs with high fiber apparent digestibility, which provided a theoretical basis and reference for further understanding the impact of gut microbiota on fiber digestibility of pigs.},
}

@article {pmid34867854,
year = {2021},
author = {Dat, TTH and Steinert, G and Cuc, NTK and Smidt, H and Sipkema, D},
title = {Bacteria Cultivated From Sponges and Bacteria Not Yet Cultivated From Sponges-A Review.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {737925},
doi = {10.3389/fmicb.2021.737925},
pmid = {34867854},
issn = {1664-302X},
abstract = {The application of high-throughput microbial community profiling as well as "omics" approaches unveiled high diversity and host-specificity of bacteria associated with marine sponges, which are renowned for their wide range of bioactive natural products. However, exploration and exploitation of bioactive compounds from sponge-associated bacteria have been limited because the majority of the bacteria remains recalcitrant to cultivation. In this review, we (i) discuss recent/novel cultivation techniques that have been used to isolate sponge-associated bacteria, (ii) provide an overview of bacteria isolated from sponges until 2017 and the associated culture conditions and identify the bacteria not yet cultured from sponges, and (iii) outline promising cultivation strategies for cultivating the uncultivated majority of bacteria from sponges in the future. Despite intensive cultivation attempts, the diversity of bacteria obtained through cultivation remains much lower than that seen through cultivation-independent methods, which is particularly noticeable for those taxa that were previously marked as "sponge-specific" and "sponge-enriched." This poses an urgent need for more efficient cultivation methods. Refining cultivation media and conditions based on information obtained from metagenomic datasets and cultivation under simulated natural conditions are the most promising strategies to isolate the most wanted sponge-associated bacteria.},
}

@article {pmid34867852,
year = {2021},
author = {Oh, BS and Choi, WJ and Kim, JS and Ryu, SW and Yu, SY and Lee, JS and Park, SH and Kang, SW and Lee, J and Jung, WY and Kim, YM and Jeong, JH and Lee, JH},
title = {Cell-Free Supernatant of Odoribacter splanchnicus Isolated From Human Feces Exhibits Anti-colorectal Cancer Activity.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {736343},
doi = {10.3389/fmicb.2021.736343},
pmid = {34867852},
issn = {1664-302X},
abstract = {The gut microbiota (GM) has been shown to be closely associated with the development of colorectal cancer (CRC). However, the involvement of GM is CRC has mainly been demonstrated by metagenomic profiling studies showing the compositional difference between the GM of healthy individuals and that of CRC patients and not by directly studying isolated gut microbes. Thus, to discover novel gut microbes involved in CRC, we isolated the GM from the feces of healthy individuals and evaluated its anti-CRC activity in vitro and in vivo. After GM isolation, cell-free supernatants (CFSs) were prepared from the isolated gut microorganisms to efficiently screen a large amount of the GM for anti-proliferative ability in vitro. Our results showed that the CFSs of 21 GM isolates had anti-proliferative activity against human colon cancer HCT 116 cells. Of these 21 GM isolates, GM07 was chosen for additional study because it had the highest anti-cancer activity against mouse colon cancer CT 26 cells in vitro and was further evaluated in a CT 26 allograft mouse model in vivo. GM07 was identified as Odoribacter splanchnicus through phylogenetic analysis based on 16S rRNA gene sequencing. Further investigation determined that the CFS of O. splanchnicus (OsCFS) induced anti-proliferative activity via apoptosis, but not cell cycle arrest. Moreover, GC/MS analysis suggested that the putative active molecule in OsCFS is malic acid. Finally, in the CRC mouse model, peri-tumoral injection of OsCFS significantly decreased CRC formation, compared to the control group. Altogether, these findings will provide valuable information for the discovery of potential probiotic candidates that inhibit CRC.},
}

@article {pmid34867834,
year = {2021},
author = {Thomas, P and Sahu, PK},
title = {Vertical Transmission of Diverse Cultivation-Recalcitrant Endophytic Bacteria Elucidated Using Watermelon Seed Embryos.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {635810},
doi = {10.3389/fmicb.2021.635810},
pmid = {34867834},
issn = {1664-302X},
abstract = {Seed transmission of endophytic microorganisms is a growing research area in plant biology and microbiology. We employed cultivation versus cultivation-independent approaches on excised embryos from watermelon seeds (6-12 months in storage) and on embryo-derived in vitro seedlings (EIVS) to assess the vertical transmission of endophytic bacteria. Surface-disinfected watermelon seeds bore abundant residual bacteria in the testa and perisperm tissues, predominantly Bacillus spp. propounding the essentiality of excluding all non-embryonic tissues for vertical transmission studies. Tissue homogenates from re-disinfected seed embryos displayed no cultivable bacteria during the 1-week monitoring. Bright-field live microscopy revealed abundant bacteria in tissue homogenates and in embryo sections as intracellular motile particles. Confocal imaging on embryo sections after SYTO-9 staining and eubacterial fluorescent in situ hybridization (FISH) endorsed enormous bacterial colonization. Quantitative Insights Into Microbial Ecology (QIIME)-based 16S rRNA V3-V4 taxonomic profiling excluding the preponderant chloroplast and mitochondrial sequences revealed a high bacterial diversity in watermelon seed embryos mainly Firmicutes barring spore formers followed by Proteobacteria, Bacteroidetes, and Actinobacteria, and other minor phyla. Embryo-base (comprising the radicle plus plumule parts) and embryo-cotyledon parts differed in bacterial profiles with the abundance of Firmicutes in the former and Proteobacteria dominance in the latter. EIVS displayed a higher bacterial diversity over seed embryos indicating the activation from the dormant stage of more organisms in seedlings or their better amenability to DNA techniques. It also indicated embryo-to-seedling bacterial transmission, varying taxonomic abundances for seed embryos and seedlings, and differing phylogenic profiles for root, hypocotyl, and cotyledon/shoot-tip tissues. Investigations on different watermelon cultivars confirmed the embryo transmission of diverse cultivation recalcitrant endophytic bacteria. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes formed the core phyla across different cultivars with 80-90% similarity at genus to phylum levels. Conversely, freshly harvested seeds displayed a dominance of Proteobacteria. The findings revealed that dicot seeds such as in different watermelon cultivars come packaged with abundant and diverse vertical and seedling-transmissible cultivation recalcitrant endophytic bacteria with significant implications for plant biology.},
}

@article {pmid34866919,
year = {2021},
author = {Chen, H and Bai, X and Gao, Y and Liu, W and Yao, X and Wang, J},
title = {Profile of Bacteria with ARGs Among Real-World Samples from ICU Admission Patients with Pulmonary Infection Revealed by Metagenomic NGS.},
journal = {Infection and drug resistance},
volume = {14},
number = {},
pages = {4993-5004},
doi = {10.2147/IDR.S335864},
pmid = {34866919},
issn = {1178-6973},
abstract = {Background: Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by antibiotic resistance pathogens. A thorough and up-to-date knowledge of the local spectrum of antibiotic resistant bacteria can improve the antibiotic treatment efficiency. In this study, we aimed to reveal the profile of bacteria with antibiotic resistance genes (ARGs) in real-world samples from ICU admission patients with pulmonary infection in Mainland, China, by metagenomic next-generation sequencing (mNGS).

Methods: A total of 504 different types of clinical samples from 452 ICU admission patients with pulmonary infection were detected by mNGS analysis.

Results: A total of 485 samples from 434 patients got successful mNGS results. Among 434 patients, one or more bacteria with ARGs were detected in 192 patients (44.24%, 192/434), and ≥2 bacteria with ARGs were detected in 85 (19.59%, 85/434) patients. The predominant detected bacteria were Corynebacterium striatum (C. striatum) (11.76%, 51/434), Acinetobacter baumannii (A. baumannii) (11.52%, 50/434) and Enterococcus faecium (E. faecium) (8.99%, 39/434). ermX conferred resistance to MSLB and cmx to phenicol were the only two ARGs detected in C. striatum; in A. baumannii, most of ARGs were resistance-nodulation-division (RND)-type efflux pumps genes, which conferred resistance to multi-drug; ermB conferred resistance to MSLB and efmA to multi-drug were the predominant ARGs in E. faecium. Bacteria with ARGs were detected in 50% (140/280) bronchoalveolar lavage fluid (BALF) and 50.5% (48/95) sputum samples, which were significantly higher than in blood and cerebrospinal fluid (CSF) samples.

Conclusion: High level of bacteria with ARGs was observed in clinical samples, especially BALF and sputum samples from ICU admission patients with pulmonary infection in Mainland, China. And C. striatum resistant to MSLB and/or phenicol, multi-drug resistance A. baumannii and E. faecium were the lead bacteria.},
}

@article {pmid34866561,
year = {2021},
author = {Marvil, CE and Babiker, A and Preston, A and Webster, A and Guarner, J and Love, K and Ghonim, E and Rebolledo, PA and Wang, YF and Arthur, RA and Johnston, HR and Waggoner, JJ and Piantadosi, A and Jacob, JT},
title = {Outbreak of SARS-CoV-2 in hospitalized hemodialysis patients: an epidemiologic and genomic investigation.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-14},
doi = {10.1017/ice.2021.465},
pmid = {34866561},
issn = {1559-6834},
abstract = {We performed an epidemiological investigation and SARS-CoV-2 genome sequencing to define the source and scope of an outbreak in a cluster of hospitalized patients. Lack of appropriate respiratory hygiene led to SARS-CoV-2 transmission to patients and healthcare workers during a single hemodialysis session, highlighting the importance of infection prevention precautions.},
}

@article {pmid34865900,
year = {2021},
author = {Zhu, F and Yan, Y and Doyle, E and Zhu, C and Jin, X and Chen, Z and Wang, C and He, H and Zhou, D and Gu, C},
title = {Microplastics altered soil microbiome and nitrogen cycling: The role of phthalate plasticizer.},
journal = {Journal of hazardous materials},
volume = {},
number = {},
pages = {127944},
doi = {10.1016/j.jhazmat.2021.127944},
pmid = {34865900},
issn = {1873-3336},
abstract = {Microplastics are emerging contaminants that are increasingly detected in soil environment, but their impact on soil microbiota and related biogeochemical processes remains poorly understood. In particular, the mechanisms involved (e.g., the role of chemical additives) are still elusive. In this study, we found that plasticizer-containing polyvinyl chloride (PVC) microplastics at 0.5% (w/w) significantly increased soil NH4+-N content and decreased NO3--N content by up to 91%, and shaped soil microbiota into a microbial system with more nitrogen-fixing microorganisms (as indicated by nifDHK gene abundance), urea decomposers (ureABC genes and urease activity) and nitrate reducers (nasA, NR, NIT-6 and napAB genes), and less nitrifiers (amoC gene and potential nitrification rate). Exposure to plasticizer alone had a similar effect on soil nitrogen parameters but microplastics of pure PVC polymer (either granule or film) had little effect over 60 days, indicating that phthalate plasticizer released from microplastics was the main driver of effects observed. Furthermore, a direct link between phthalate plasticizer, microbial taxonomic changes and altered nitrogen metabolism was established by the isolation of phthalate-degrading bacteria involved in nitrogen cycling. This study highlights the importance of chemical additives in determining the interplay of microplastics with microbes and nutrient cycling, which needs to be considered in future studies.},
}

@article {pmid34865800,
year = {2021},
author = {Zhang, Z and Han, Z and Wu, Y and Jiang, S and Ma, C and Zhang, Y and Zhang, J},
title = {Metagenomics assembled genome scale analysis revealed the microbial diversity and genetic polymorphism of Lactiplantibacillus plantarum in traditional fermented foods of Hainan, China.},
journal = {Food research international (Ottawa, Ont.)},
volume = {150},
number = {Pt A},
pages = {110785},
doi = {10.1016/j.foodres.2021.110785},
pmid = {34865800},
issn = {1873-7145},
abstract = {Exploring the microbiome in fermented foods and their effects on food quality and sustainability is beneficial to provide data support for understanding how they affects human physiology. Here, metagenomic sequencing and metagenomic assembled genomes (MAGs) were applied to appraise the microbial diversity of fermented Yucha (FYC) and fermented vegetables (FVE). The antibiotic resistance genes (ARGs) enrichment and genetic polymorphism of Lactiplantibacillus plantarum in fermented foods of different regions were compared. The results showed that Lactiplantibacillus plantarum was the dominant species in FYC, while Lactiplantibacillus fermentum in FVE occupied the dominant position. From 32 high-quality MAGs, the central differential Lactic acid bacteria were higher in FVE. By comparing the Lactiplantibacillus plantarum MAGs in Hainan and Other regions, we found that the total Single Nucleotide Polymorphisms of Lactiplantibacillus plantarum in Hainan were significantly higher than other areas. Six non-synonymous mutations were included in the primary differential mutation, especially TrkA family potassium uptake protein and MerR family transcriptional regulator, which may be related to the hypersaline environment and highest ARGs enrichment in Hainan. This research provides valuable insight into our understanding of the microbiome of fermented food. Meanwhile, the analysis of Lactiplantibacillus plantarum genetic polymorphism based on MAGs helps us understand this strain's evolutionary history.},
}

@article {pmid34865013,
year = {2021},
author = {Kindler, GS and Wong, HL and Larkum, AWD and Johnson, M and MacLeod, FI and Burns, BP},
title = {Genome-resolved metagenomics provides insights into the functional complexity of microbial mats in Blue Holes, Shark Bay.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiab158},
pmid = {34865013},
issn = {1574-6941},
abstract = {The present study describes for the first time the community composition and functional potential of the microbial mats found in the supratidal, gypsum-rich, and hypersaline region of Blue Holes, Shark Bay. This was achieved via high throughput metagenomic sequencing of total mat community DNA and complementary analyses using hyperspectral confocal microscopy. Mat communities were dominated by Proteobacteria (29%), followed by Bacteroidetes/Chlorobi Group (11%), and Planctomycetes (10%). These mats were found to also harbor a diverse community of potentially novel microorganisms including members from the DPANN, Asgard archaea, and Candidate Phyla Radiation, with highest diversity found in the lower regions (∼14-20 mm depth) of the mat. In addition to pathways for major metabolic cycles, a range of putative rhodopsins with previously uncharacterized motifs and functions were identified along with heliorhodopsins and putative schizorhodopsins. Critical microbial interactions were also inferred, and from 117 medium-to-high quality metagenome-assembled genomes (MAGs), viral defense mechanisms (CRISPR, BREX, and DISARM), elemental transport, osmoprotection, heavy metal and UV resistance were also detected. These analyses have provided a greater understanding of these distinct mat systems in Shark Bay, including key insights into adaptive responses and proposing that photoheterotrophy may be an important lifestyle in Blue Holes.},
}

@article {pmid34864967,
year = {2021},
author = {Sato, Y and Takebe, H and Tominaga, K and Oishi, K and Kumagai, H and Yoshida, T and Hirooka, H},
title = {Taxonomic and functional characterization of the rumen microbiome of Japanese Black cattle revealed by 16S rRNA gene amplicon and metagenome shotgun sequencing.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiab152},
pmid = {34864967},
issn = {1574-6941},
abstract = {This study aimed to determine the taxonomic and functional characteristics of the Japanese Black steer rumen microbiome. The rumen microbiomes of six Japanese Black steers (age 14.7 ± 1.44 mo) and six Japanese Black sires × Holstein dams crossbred (F1) steers (age 11.1 ± 0.39 mo), fed the same diet, were evaluated. Based on 16S rRNA gene sequencing, the beta diversity revealed differences in microbial community structures between the Japanese Black and F1 rumen. Shotgun sequencing showed that Fibrobacter succinogenes and two Ruminococcus spp., which are related to cellulose degradation were relatively more abundant in the Japanese Black steer rumen than in the F1 rumen. Furthermore, the 16S rRNA gene copy number of F. succinogenes was significantly higher in the Japanese Black steer rumen than in the F1 rumen according to quantitative real-time polymerase chain reaction analysis. Genes encoding the enzymes that accelerate cellulose degradation and those associated with hemicellulose degradation were enriched in the Japanese Black steer rumen. Although Prevotella spp. were predominant both in the Japanese Black and F1 rumen, the genes encoding carbohydrate-active enzymes of Prevotella spp. may differ between Japanese Black and F1.},
}

@article {pmid34864203,
year = {2021},
author = {Maran, MIJ and Davis G, DJ},
title = {Benefits of merging paired-end reads before pre-processing environmental metagenomics data.},
journal = {Marine genomics},
volume = {61},
number = {},
pages = {100914},
doi = {10.1016/j.margen.2021.100914},
pmid = {34864203},
issn = {1876-7478},
abstract = {BACKGROUND: High throughput sequencing of environmental DNA has applications in biodiversity monitoring, taxa abundance estimation, understanding the dynamics of community ecology, and marine species studies and conservation. Environmental DNA, especially, marine eDNA, has a fast degradation rate. Aside from the good quality reads, the data could have a significant number of reads that fall slightly below the default PHRED quality threshold of 30 on sequencing. For quality control, trimming methods are employed, which generally precede the merging of the read pairs. However, in the case of eDNA, a significant percentage of reads within the acceptable quality score range are also dropped.

METHODS: To infer the ideal merge tool that is sensitive to eDNA, two Hiseq paired-end eDNA datasets were utilized to study the merging by the tools - FLASH (Fast Length Adjustment of SHort reads), PANDAseq, COPE, BBMerge, and VSEARCH without preprocessing. We assessed these tools on the following parameters: Time taken to process, the quality, and the number of merged reads. Trimmomatic, a widely-used preprocessing tool, was also assessed by preprocessing the datasets at different parameters for the two approaches of preprocessing: Sliding Window and Maximum Information. The preprocessed read pairs were then merged using the ideal merge tool identified earlier.

RESULTS: FLASH is the most efficient merge tool balancing data conservation, quality of reads, and processing time. We compared Trimmomatic's two quality trimming options with increasing strictness with FLASH's direct merge. The raw reads processed with Trimmomatic then merged, yielded a significant drop in reads compared to the direct merge. An average of 29% of reads was dropped when directly merged with FLASH. Maximum Information option resulted in 30.7% to 68.05% read loss with lowest and highest stringency parameters, respectively. The Sliding Window approach conserves approximately 10% more reads at a PHRED score of 25 set as the threshold for a window of size 4. The lowered PHRED cut off conserves about 50% of the reads that could potentially be informative. We noted no significant reduction of data while optimizing the number of reads read in a window with the ideal quality (Q) score.

CONCLUSIONS: Losing reads can negatively impact the downstream processing of the environmental data, especially for sequence alignment studies. The quality trim-first-merge-later approach can significantly decrease the number of reads conserved. However, direct merging of pair-end reads using FLASH conserved more than 60% of the reads. Therefore, direct merging of the paired-end reads can prevent potential removal of informative reads that do not comply by the trimming tool's strict checks. FLASH to be an efficient tool in conserving reads while carrying out quality trimming in moderation. Overall, our results show that merging paired-end reads of eDNA data before trimming can conserve more reads.},
}

@article {pmid34864185,
year = {2021},
author = {Meng, X and Cao, Q and Sun, Y and Huang, S and Liu, X and Li, D},
title = {16S rRNA genes- and metagenome-based confirmation of syntrophic butyrate-oxidizing methanogenesis enriched in high butyrate loading.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {126483},
doi = {10.1016/j.biortech.2021.126483},
pmid = {34864185},
issn = {1873-2976},
abstract = {The understanding and enrichment of consortia formed by syntrophic butyrate-oxidizing bacteria and methanogens in the complex environment are crucial for effectively degrading butyrate and preventing acid inhibition. In this study, the better butyrate-tolerated and highly efficient microbial consortia were domesticated and enriched through adding butyric acid ranging from 0.2 to 4.4 g/(L·d). The volumetric biogas production continuously increased to 1.65 L/(L·d). Microbial community diversity showed that a dramatic shift of bacterial structure occurred at BAL of 1.6 g/(L·d) and the structure presented better stability at high BAL. The syntrophic consortia and the main metabolic pathways were revealed through combination of the 16S rDNA and metagenome sequencing analyses. Syntrophomonas was the major butyrate-oxidizing bacterium and oxidized butyrate mainly through β-oxidaiton. Synergistaceae and Mesotoga acted as the main acetate-oxidizing bacteria. IHT and methanogenesis pathways were strongly enhanced by DMER64 and Methanosarcina as the main H2 carrier and dominant methanogen, respectively.},
}

@article {pmid34864022,
year = {2021},
author = {Buta-Hubeny, M and Korzeniewska, E and Hubeny, J and Zieliński, W and Rolbiecki, D and Harnisz, M and Paukszto, Ł},
title = {Structure of the manure resistome and the associated mobilome for assessing the risk of antimicrobial resistance transmission to crops.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {152144},
doi = {10.1016/j.scitotenv.2021.152144},
pmid = {34864022},
issn = {1879-1026},
abstract = {In this study, the impact of bovine and poultry manure on the quantitative and qualitative composition of antibiotic resistance genes (ARGs) and the environmental mobilome associated with antimicrobial resistance in soil and crops was determined with the use of next generation sequencing methods. The aim of the study was to perform a metagenomic analysis of manure to estimate the risk of the transmission of ARGs and bacterial drug resistance carriers to fertilized soil and crops. The total copy number of ARGs was nearly four times higher in poultry manure (555 ppm) than in bovine manure (140 ppm), and this relationship was also noted in fertilized soil. Poultry manure induced a much greater increase in the concentrations of ARGs in the soil environment (196.4 ppm) than bovine manure (137.8 ppm) immediately after supplementation. The application of poultry manure led to the highest increase in the abundance of genes encoding resistance to tetracyclines (9%), aminoglycosides (3.5%), sulfonamides (3%), bacitracin (2%), chloramphenicol (2%), and macrolide-lincosamide-streptogramin antibiotics (1%). Heavy metals were stronger promoters of antibiotic resistance in the environment than antibiotics. Antibiotics exerted a greater influence on maintaining the diversity of ARGs than on increasing their abundance in soil. Large quantities of insertion sequences (IS), including those associated with the mobility of ARGs in the population of ESKAPEE pathogens, are introduced to soil with manure. These IS remain stable for up to several months, which indicates that manure, in particular poultry manure, significantly increases the risk of rapid ARG transfer to the environment. Manure also largely contributes to an increase in the diversity of the resistome and mobilome in the metagenome of bacteria isolated from crops. Bacteria of the phylum Proteobacteria appear to play a major role in the transmission of multiple ARGs in crops grown for human and animal consumption.},
}

@article {pmid34864011,
year = {2021},
author = {Eze, MO and Thiel, V and Hose, GC and George, SC and Daniel, R},
title = {Enhancing rhizoremediation of petroleum hydrocarbons through bioaugmentation with a plant growth-promoting bacterial consortium.},
journal = {Chemosphere},
volume = {289},
number = {},
pages = {133143},
doi = {10.1016/j.chemosphere.2021.133143},
pmid = {34864011},
issn = {1879-1298},
abstract = {The slow rate of natural attenuation of organic pollutants, together with unwanted environmental impacts of traditional remediation strategies, has necessitated the exploration of plant-microbe systems for enhanced bioremediation applications. The identification of microorganisms capable of promoting rhizoremediation through both plant growth-promoting and hydrocarbon-degrading processes is crucial to the success and adoption of plant-based remediation techniques. In this study, through successive enrichments of soil samples from a historic oil-contaminated site in Wietze, Germany, we isolated a plant growth-promoting and hydrocarbon-degrading bacterial consortium dominated by Alphaproteobacteria. In microcosm experiments involving Medicago sativa L. and the isolated bacterial consortium, we examined the ability of the consortium to enhance rhizoremediation of petroleum hydrocarbons. The inoculation of M. sativa with the consortium resulted in 66% increase in plant biomass, and achieved a 91% reduction in diesel fuel hydrocarbon concentrations in the soil within 60 days. Metagenome analysis led to the identification of genes and taxa putatively involved in these processes. The majority of the coding DNA sequences associated with plant growth promotion and hydrocarbon degradation in this study were affiliated to Acidocella aminolytica and Acidobacterium capsulatum indicating their potential for biotechnological applications in the rhizoremediation of sites contaminated by petroleum-derived organic pollutants.},
}

@article {pmid34863851,
year = {2021},
author = {Ricardo Soccol, C and Sthepani Orozco Colonia, B and Vinícius de Melo Pereira, G and Daniel Goyzueta Mamani, L and Grace Karp, S and Thomaz Soccol, V and de Oliveira Penha, R and José Dalmas Neto, C and César de Carvalho, J},
title = {Bioprospecting lipid-producing microorganisms: from metagenomic-assisted isolation techniques to industrial application and innovations.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {126455},
doi = {10.1016/j.biortech.2021.126455},
pmid = {34863851},
issn = {1873-2976},
abstract = {Traditionally, lipid-producing microorganisms have been obtained via conventional bioprospecting based on isolation and screening techniques, demanding time and effort. Thus, high-throughput sequencing combined with conventional microbiological approaches has emerged as an advanced and rapid strategy for recovering novel oleaginous microorganisms from target environments. This review highlights recent developments in lipid-producing microorganism bioprospecting, following (i) from traditional cultivation techniques to state-of-the-art metagenomics approaches; (ii) related topics on workflow, next-generation sequencing platforms, and knowledge bioinformatics; and (iii) biotechnological potential of the production of docosahexaenoic acid (DHA) by Aurantiochytrium limacinum, arachidonic acid (ARA) by Mortierella alpina and biodiesel by Rhodosporidium toruloides. These three species have been shown to be highly promising and studied in research articles, patents and commercialized products. Trends, innovations and future perspectives of these microorganisms are also addressed. Thus, these microbial lipids allow the development of food, feed and biofuels as alternative solutions to animal and vegetable oils.},
}

@article {pmid34863018,
year = {2021},
author = {Pelsma, KAJ and In 't Zandt, MH and Op den Camp, HJM and Jetten, MSM and Dean, JF and Welte, CU},
title = {Amsterdam urban canals contain novel niches for methane-cycling microorganisms.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.15864},
pmid = {34863018},
issn = {1462-2920},
abstract = {Urbanised environments have been identified as hotspots of anthropogenic methane emissions. Especially urban aquatic ecosystems are increasingly recognised as important sources of methane. However, the microbiology behind these emissions remains unexplored. Here, we applied microcosm incubations and molecular analyses to investigate the methane-cycling community of the Amsterdam canal system in the Netherlands. The sediment methanogenic communities were dominated by Methanoregulaceae and Methanosaetaceae, with co-occurring methanotrophic Methanoperedenaceae and Methylomirabilaceae indicating the potential for anaerobic methane oxidation. Methane was readily produced after substrate amendment, suggesting an active but substrate-limited methanogenic community. Bacterial 16 S rRNA gene amplicon sequencing of the sediment revealed a high relative abundance of Thermodesulfovibrionia. Canal wall biofilms showed the highest initial methanotrophic potential under oxic conditions compared to the sediment. During prolonged incubations the maximum methanotrophic rate increased to 8.08 mmol gDW -1 d-1 that was concomitant with an enrichment of Methylomonadaceae bacteria. Metagenomic analysis of the canal wall biofilm lead to the recovery of a single methanotroph metagenome-assembled genome. Taxonomic analysis showed that this methanotroph belongs to the genus Methyloglobulus Our results underline the importance of previously unidentified and specialised environmental niches at the nexus of the natural and human-impacted carbon cycle. This article is protected by copyright. All rights reserved.},
}

@article {pmid34862696,
year = {2021},
author = {Jiao, S and Chen, W and Wei, G},
title = {Core microbiota drive functional stability of soil microbiome in reforestation ecosystems.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.16024},
pmid = {34862696},
issn = {1365-2486},
abstract = {Revealing the ecological roles of core microbiota in the maintenance of the functional stability of soil microbiomes is crucial for sustainable ecosystem functioning; however, there is a dearth of whole-soil profile studies on the fundamental topic in microbial ecology, especially in the context of ecological restoration. Here, we explored whether core microbiota influence the temporal changes in the functional stability of soil microbiomes throughout the soil profile (i.e., soil depths of 0-300 cm) during natural succession in restored ex-arable ecosystems, via high-throughput amplicon and metagenomic sequencing. We revealed that core microbiota were essential for the maintenance of the functional stability of soil microbiomes in reforestation ecosystems. Specifically, the core taxa within one cluster of soil network, which had similar ecological preferences, had major contributions to functional stability. Reforestation significantly decreased the functional stability of soil microbiomes, which exhibited significant variations along the vertical soil profile in the reforested soils. Overall, the findings enhance our understanding of the factors driving functional stability in soil microbiomes, and suggests that core microbiota should be considered a key factor and integrated in policy and management activities targeting the enhancement and maintenance of functional stability and ecosystem sustainability in ecological restoration programs.},
}

@article {pmid34862647,
year = {2021},
author = {Tyx, RE and Rivera, AJ and Stanfill, SB and Zaatari, GS and Watson, CH},
title = {Shotgun metagenome sequencing of a Sudanese toombak snuff tobacco: Genetic attributes of a high tobacco-specific nitrosamine (TSNA) containing smokeless tobacco product.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/lam.13623},
pmid = {34862647},
issn = {1472-765X},
abstract = {The most alarming aspect of the Sudanese toombak smokeless tobacco is that it contains high levels of highly toxic Tobacco-Specific Nitrosamines (TSNAs). Understanding the microbiology of toombak is of relevance because TSNAs are an indirect result of microbial-mediated nitrate reductions. We conducted shotgun metagenomic sequencing on a toombak product for which relevant features are presented here. The microbiota was composed of over 99% Bacteria. The most abundant taxa included Actinobacteria, specifically genera Enteractinococcus and Corynebacterium, while Firmicutes were represented by Family Bacillaceae and the genus Staphylococcus. Selected gene targets were nitrate reduction and transport, antimicrobial resistance, and other genetic transference mechanisms. Canonical nitrate reduction and transport genes (i.e., nar) were found for Enteractinococcus and Corynebacterium while various species of Staphylococcus exhibited a notable number of antimicrobial resistance and genetic transference genes. The nitrate reduction activity of the microbiota in toombak is suspected to be a contributing factor to its high levels of TSNAs. Additionally, the presence of antimicrobial resistance and transference genes could contribute to deleterious effects on oral and gastrointestinal health of the end user. Overall, the high toxicity and increased incidences of cancer and oral disease of toombak users warrants further investigation into the microbiology of toombak.},
}

@article {pmid34862599,
year = {2021},
author = {Li, Y and Zhao, D and Qian, M and Liu, J and Pan, C and Zhang, X and Duan, X and Zhang, Y and Jia, W and Wang, L},
title = {Amlodipine, an anti-hypertensive drug, alleviates non-alcoholic fatty liver disease by modulating gut microbiota.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.15768},
pmid = {34862599},
issn = {1476-5381},
abstract = {BACKGROUND AND PURPOSE: Non-alcoholic fatty liver disease (NAFLD) represents a severe public health problem. It often coexists with hypertension in the context of metabolic syndrome. Here, we investigated the effects of amlodipine on non-alcoholic fatty liver disease combined with hypertension and the underlying mechanism.

EXPERIMENTAL APPROACH: mice were fed with high-fat diet and 0.05% N-Nitro-L-arginine methylester sterile water to induce NAFLD with hypertension. Gut microbiota composition and function were assessed by 16S ribosomal DNA and metagenomic sequencing. Untargeted metabolome profiles were applied to identify differential metabolites in mice cecum.

KEY RESULTS: Amlodipine besylate (AB) and amlodipine aspartate (AA) significantly decreased liver injury, hepatic steatosis and improved lipid metabolism with a concomitant reduction in the expression of lipogenic genes in mice with NAFLD and hypertension. Mechanistically, AA and AB have potential in restoring intestinal barrier integrity and improving antimicrobial defense along with the elevated abundances of Akkermansia, Bacteroides and Lactobacillus. Noteworthily, the gut microbiota in AB and AA-treated mice had higher abundance of functional genes involved in taurine and hypotaurine metabolism. Consistently, the strengthened taurine and hypotaurine metabolism was confirmed by the untargeted metabolome analysis. Based on the correlation and causal analysis, the altered gut microbiota composition and the enhancement of taurine and hypotaurine metabolism may synergistically decreased ALT, liver triglycerides, lipogenic genes and plasma cholesterol in HFD-fed hypertensive mice.

CONCLUSION AND IMPLICATIONS: Collectively, AA and AB exert multi-factorial improvements in NAFLD and hypertension by modulating gut microbiota, and may serve as a promising therapeutic agent for treating these diseases.},
}

@article {pmid34862584,
year = {2021},
author = {Lu, Z and Su, H},
title = {Employing gene chip technology for monitoring and assessing soil heavy metal pollution.},
journal = {Environmental monitoring and assessment},
volume = {194},
number = {1},
pages = {2},
pmid = {34862584},
issn = {1573-2959},
support = {SXDJ2019//key laboratory of degraded and unused land consolidation engineering, and the ministry of natural and resources/ ; },
abstract = {Soil heavy metals pollution can cause many serious environment problems because of involving a very complex pollution process for soil health. Therefore, it is very important to explore methods that can effectively evaluate heavy metal pollution. Researchers were actively looking for new ideas and new methods for evaluating and predicting levels of soil heavy metal pollution. The study on microbial communities is one of the effective methods using gene chip technology. Gene chip technology, as a high-throughput metagenomics analysis technique, has been widely used for studying the structure and function of complex microbial communities in different polluted environments from different pollutants, including the soil polluted by heavy metals. However, there is still a lack of a systematic summarization for the polluted soil by heavy metals. This paper systematically analyzed soil heavy metals pollution via reviewing previous studies on applying gene chip technology, including single species, tolerance mechanisms, enrichment mechanisms, anticipation and evaluation of soil remediation, and multi-directional analysis. The latest gene chip technologies and corresponding application cases for discovering critical species and functional genes via analyzing microbial communities and evaluating heavy metal pollution of soil were also introduced in this paper. This article can provide scientific guidance for researchers actively investigating the soil polluted by heavy metals.},
}

@article {pmid34862473,
year = {2021},
author = {Maza-Márquez, P and Lee, MD and Detweiler, AM and Bebout, BM},
title = {Millimeter-scale vertical partitioning of nitrogen cycling in hypersaline mats reveals prominence of genes encoding multi-heme and prismane proteins.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {34862473},
issn = {1751-7370},
abstract = {Microbial mats are modern analogues of the first ecosystems on the Earth. As extant representatives of microbial communities where free oxygen may have first been available on a changing planet, they offer an ecosystem within which to study the evolution of biogeochemical cycles requiring and inhibited by oxygen. Here, we report the distribution of genes involved in nitrogen metabolism across a vertical oxygen gradient at 1 mm resolution in a microbial mat using quantitative PCR (qPCR), retro-transcribed qPCR (RT-qPCR) and metagenome sequencing. Vertical patterns in the presence and expression of nitrogen cycling genes, corresponding to oxygen requiring and non-oxygen requiring nitrogen metabolism, could be seen across gradients of dissolved oxygen and ammonium. Metagenome analysis revealed that genes annotated as hydroxylamine dehydrogenase (proper enzyme designation EC 1.7.2.6, hao) and hydroxylamine reductase (hcp) were the most abundant nitrogen metabolism genes in the mat. The recovered hao genes encode hydroxylamine dehydrogenase EC 1.7.2.6 (HAO) proteins lacking the tyrosine residue present in aerobic ammonia oxidizing bacteria (AOB). Phylogenetic analysis confirmed that those proteins were more closely related to ɛHao protein present in Campylobacterota lineages (previously known as Epsilonproteobacteria) rather than oxidative HAO of AOB. BLAST analysis of some transcribed proteins indicated that they likely functioned as a nitrate reductase. The presence of hao sequences related with ɛHao protein, as well as numerous hcp genes encoding a prismane protein, suggest the presence of a nitrogen cycling pathway previously described in Nautilia profundicola as ancestral to the most commonly studied present day nitrogen cycling pathways.},
}

@article {pmid34862421,
year = {2021},
author = {Palomba, A and Tanca, A and Abbondio, M and Sau, R and Serra, M and Marongiu, F and Fraumene, C and Pagnozzi, D and Laconi, E and Uzzau, S},
title = {Time-restricted feeding induces Lactobacillus- and Akkermansia-specific functional changes in the rat fecal microbiota.},
journal = {NPJ biofilms and microbiomes},
volume = {7},
number = {1},
pages = {85},
pmid = {34862421},
issn = {2055-5008},
support = {FAR 2019/2020//Università degli Studi di Sassari (University of Sassari)/ ; },
abstract = {Diet is a key factor influencing gut microbiota (GM) composition and functions, which in turn affect host health. Among dietary regimens, time-restricted (TR) feeding has been associated to numerous health benefits. The impact of TR feeding on the GM composition has been mostly explored by means of metagenomic sequencing. To date, however, little is known about the modulation of GM functions by this dietary regimen. Here, we analyzed the effects of TR feeding on GM functions by evaluating protein expression changes in a rat model through a metaproteomic approach. We observed that TR feeding has a relevant impact on GM functions, specifically leading to an increased abundance of several enzymes involved in carbohydrate and protein metabolism and expressed by Lactobacillus spp. and Akkermansia muciniphila. Taken together, these results contribute to deepening our knowledge about the key relationship between diet, GM, and health.},
}

@article {pmid34862253,
year = {2021},
author = {Dutta, M and Lim, JJ and Cui, JY},
title = {PXR and the gut-liver axis: a recent update.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {},
number = {},
pages = {},
doi = {10.1124/dmd.121.000415},
pmid = {34862253},
issn = {1521-009X},
abstract = {It is well-known that the pregnane X receptor (PXR/Nr1i2) is a critical xenobiotic-sensing nuclear receptor enriched in liver and intestine and is responsible for drug-drug interactions (DDI), due to their versatile ligand binding domain (LBD) and target genes involved in xenobiotic biotransformation. PXR can be modulated by various xenobiotics including pharmaceuticals, nutraceuticals, dietary factors, and environmental chemicals. Microbial metabolites such as certain secondary bile acids (BAs) and the tryptophan metabolite indole-3-propionic acid (IPA) are endogenous PXR activators. Gut microbiome is increasingly recognized as an important regulator for host xenobiotic biotransformation and intermediary metabolism. PXR regulates and is regulated by the gut-liver axis. This review summarizes recent research advancements leveraging pharmaco- and toxico-metagenomic approaches that have redefined the previous understanding of PXR. Key topics covered in this review include 1) genome-wide investigations on novel PXR-target genes, novel PXR-DNA interaction patterns, and novel PXR-targeted intestinal bacteria; 2) key PXR-modulating activators and suppressors of exogenous and endogenous sources; 3) novel bi-directional interactions between PXR and gut microbiome under physiological, pathophysiological, pharmacological, and toxicological conditions; and 4) modifying factors of PXR-signaling including species- and sex difference, and time (age, critical windows of exposure, and circadian rhythm). The review also discusses critical knowledge gaps and important future research topics centering around PXR. Significance Statement This review summarizes recent research advancements leveraging O'mics approaches that have redefined the previous understanding of the xenobiotic-sensing nuclear receptor PXR. Key topics include: 1) genome-wide investigations on novel PXR-targeted host genes and intestinal bacteria as well as novel PXR-DNA interaction patterns; 2) key PXR modulators including microbial metabolites under physiological, pathophysiological, pharmacological, and toxicological conditions; and 3) modifying factors including species, sex, and time.},
}

@article {pmid34861636,
year = {2021},
author = {Wang, XH and Yang, YN and Liang, Y and Lang, R and Zeng, Q and Yan, L and Yu, RH and Wu, CM},
title = {Structural modulation of gut microbiota during alleviation of experimental passive Heymann nephritis in rats by a traditional Chinese herbal formula.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {145},
number = {},
pages = {112475},
doi = {10.1016/j.biopha.2021.112475},
pmid = {34861636},
issn = {1950-6007},
abstract = {BACKGROUND: Jianpi-Qushi-Heluo formula (JQHF) has been used to treat idiopathic membranous nephropathy (IMN) in hospitals for many years.

PURPOSE: Elucidating the protective effect and exploring the potential mechanism of JQHF against IMN.

METHODS: Passive Heymann nephritis (PHN) was induced in rats by a single tail vein injection of anti-Fx1A antiserum. Then, the animals were treated with JQHF at 16.2 g/kg or 32.4 g/kg, with benzepril (10 mg/kg) as a positive control. Renal function was evaluated by biochemical measurements and pathological testing. Fecal samples were collected before and after treatment to analyze the gut microbiota composition by shotgun whole metagenome sequencing.

RESULTS: JQHF exhibited potent efficacy in ameliorating PHN at both doses, as revealed by decreasing the deposition of IgG and C5b-9, relieving podocyte injury, and reducing glomerular and tubular cell apoptosis. The lower dose was corresponding to the clinical dosage and showed better therapeutic effects than the higher dose. Metagenomic analysis showed that gavage with 16.2 g/kg of JQHF shifted the structure of the gut microbiota in PHN rats and significantly increased the relative abundances of Prevotella copri, Lactobacillus vaginalis and Subdoligranulum variabile. Particularly, S. variabile was strongly negatively correlated with serum levels of TC and TG, the deposition of IgG and C5b-9, and apoptosis of glomerular cells.

CONCLUSIONS: The JQHF is an effective agent for the treatment of experimental PHN. The PHN-allevating effect of JQHF is associated with specific alternation of gut microbiota.},
}

@article {pmid34861436,
year = {2021},
author = {Zhang, S and Ali, A and Su, J and Huang, T and Li, M},
title = {Performance and enhancement mechanism of redox mediator for nitrate removal in immobilized bioreactor with preponderant microbes.},
journal = {Water research},
volume = {209},
number = {},
pages = {117899},
doi = {10.1016/j.watres.2021.117899},
pmid = {34861436},
issn = {1879-2448},
abstract = {The acceleration of nitrate removal in wastewater treatment by redox mediator (RM) is greatly weakened due to wash-out loss and mass transfer resistance (low hydrophilia) of RM during operation. In this study, an RM reactor with the fixed 1-Amino-4-hydroxyanthraquinone (AHAQ) and three core strains was established and achieved high nitrate removal efficiency (NRE) under low carbon to nitrogen ratio (C/N) and short hydraulic retention time (HRT) conditions, with the maximum efficiency of 99.41% (14.00 mg L-1 h-1) and average improvement by 11.97% (1.41 mg L-1 h-1). This acceleration led to more proportion of carbon consumption by denitrifying bacteria and improved their competitiveness against others in carbon deficiency, although resulting in nitrite accumulation (NIA) in lower C/N. The RM reactor induced the decorrelation tendencies between NRE and active extracellular organics and more sensitive denitrification toward C/N, which favored the stability of effluent organics and biological activities. The increase of oxidative phosphorylation and ubiquinone and other terpenoid-quinone biosynthesis pathway suggested electron transport activity was potentially enhanced by AHAQ. Although the lower C/N deteriorated the reactor NRE, the abundances of amino acids-, fatty acids- and carbohydrate-related metabolisms (45% of the total up-regulating pathways) were enhanced to utilize carbon source effectively. Meanwhile, the enhanced phosphotransferase system facilitated the balance between carbon and nitrogen metabolism. These indicated the changes in biological strategy to grow better and resist the adverse condition. This study highlighted the superior NRE by AHAQ in an immobilized reactor with core strains and more importantly, extended the RM application in wastewater treatment.},
}

@article {pmid34861073,
year = {2022},
author = {Chellappa, SL and Engen, PA and Naqib, A and Qian, J and Vujovic, N and Rahman, N and Green, SJ and Garaulet, M and Keshavarzian, A and Scheer, FAJL},
title = {Proof-of-principle demonstration of endogenous circadian system and circadian misalignment effects on human oral microbiota.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {36},
number = {1},
pages = {e22043},
doi = {10.1096/fj.202101153R},
pmid = {34861073},
issn = {1530-6860},
support = {R01HL118601/GF/NIH HHS/United States ; 1UL1TR001102/GF/NIH HHS/United States ; K99HL148500/GF/NIH HHS/United States ; R01DK099512/GF/NIH HHS/United States ; R01DK102696/GF/NIH HHS/United States ; R01HL140574/GF/NIH HHS/United States ; R01DK105072/GF/NIH HHS/United States ; #1-17-PDF-103//American Diabetes Association/ ; SAF2017-84135-R//The Spanish Government of Investigation, Development and Innovation/ ; 20795/PI/18//Seneca Foundation/ ; },
abstract = {Circadian misalignment-the misalignment between the central circadian "clock" and behavioral and environmental cycles (including sleep/wake, fasting/eating, dark/light)-results in adverse cardiovascular and metabolic effects. Potential underlying mechanisms for these adverse effects include alterations in the orogastrointestinal microbiota. However, it remains unknown whether human oral microbiota has endogenous circadian rhythms (i.e., independent of sleep/wake, fasting/eating, and dark/light cycles) and whether circadian misalignment influences oral microbiota community composition. Healthy young individuals [27.3 ± 2.3 years (18-35 years), 4 men and 2 women, body-mass index range: 18-28 kg/m2 ] were enrolled in a stringently controlled 14-day circadian laboratory protocol. This included a 32-h constant routine (CR) protocol (endogenous circadian baseline assessment), a forced desynchrony protocol with four 28-h "days" under ~3 lx to induce circadian misalignment, and a post-misalignment 40-h CR protocol. Microbiota assessments were performed on saliva samples collected every 4 h throughout both CR protocols. Total DNA was extracted and processed using high-throughput 16S ribosomal RNA gene amplicon sequencing. The relative abundance of specific oral microbiota populations, i.e., one of the five dominant phyla, and three of the fourteen dominant genera, exhibited significant endogenous circadian rhythms. Importantly, circadian misalignment dramatically altered the oral microbiota landscape, such that four of the five dominant phyla and eight of the fourteen dominant genera exhibited significant circadian misalignment effects. Moreover, circadian misalignment significantly affected the metagenome functional content of oral microbiota (inferred gene content analysis), as indicated by changes in specific functional pathways associated with metabolic control and immunity. Collectively, our proof-of-concept study provides evidence for endogenous circadian rhythms in human oral microbiota and show that even relatively short-term experimental circadian misalignment can dramatically affect microbiota community composition and functional pathways involved in metabolism and immune function. These proof-of-principle findings have translational relevance to individuals typically exposed to circadian misalignment, including night shift workers and frequent flyers.},
}

@article {pmid34860015,
year = {2021},
author = {Geng, ZQ and Qian, DK and Hu, ZY and Wang, S and Yan, Y and van Loosdrecht, MCM and Zeng, RJ and Zhang, F},
title = {Identification of Extracellular Key Enzyme and Intracellular Metabolic Pathway in Alginate-Degrading Consortia via an Integrated Metaproteomic/Metagenomic Analysis.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.1c05289},
pmid = {34860015},
issn = {1520-5851},
abstract = {Uronic acid in extracellular polymeric substances is a primary but often ignored factor related to the difficult hydrolysis of waste-activated sludge (WAS), with alginate as a typical polymer. Previously, we enriched alginate-degrading consortia (ADC) in batch reactors that can enhance methane production from WAS, but the enzymes and metabolic pathway are not well documented. In this work, two chemostats in series were operated to enrich ADC, in which 10 g/L alginate was wholly consumed. Based on it, the extracellular alginate lyase (∼130 kD, EC 4.2.2.3) in the cultures was identified by metaproteomic analysis. This enzyme offers a high specificity to convert alginate to disaccharides over other mentioned hydrolases. Genus Bacteroides (>60%) was revealed as the key bacterium for alginate conversion. A new Entner-Doudoroff pathway of alginate via 5-dehydro-4-deoxy-d-glucuronate (DDG) and 3-deoxy-d-glycerol-2,5-hexdiulosonate (DGH) as the intermediates to 2-keto-3-deoxy-gluconate (KDG) was constructed based on the metagenomic and metaproteomic analysis. In summary, this work documented the core enzymes and metabolic pathway for alginate degradation, which provides a good paradigm when analyzing the degrading mechanism of unacquainted substrates. The outcome will further contribute to the application of Bacteroides-dominated ADC on WAS methanogenesis in the future.},
}

@article {pmid34859110,
year = {2021},
author = {Horiba, K and Torii, Y and Okumura, T and Takeuchi, S and Suzuki, T and Kawada, JI and Muramatsu, H and Takahashi, Y and Ogi, T and Ito, Y},
title = {Next-Generation Sequencing to Detect Pathogens in Pediatric Febrile Neutropenia: A Single-Center Retrospective Study of 112 Cases.},
journal = {Open forum infectious diseases},
volume = {8},
number = {11},
pages = {ofab223},
pmid = {34859110},
issn = {2328-8957},
abstract = {Background: Febrile neutropenia (FN) is a frequent complication in immunocompromised patients. However, causative microorganisms are detected in only 10% of patients. This study aimed to detect the microorganisms that cause FN using next-generation sequencing (NGS) to identify the genome derived from pathogenic microorganisms in the bloodstream. Here, we implemented a metagenomic approach to comprehensively analyze microorganisms present in clinical samples from patients with FN.

Methods: FN is defined as a neutrophil count <500 cells/µL and fever ≥37.5°C. Plasma/serum samples of 112 pediatric patients with FN and 10 patients with neutropenia without fever (NE) were sequenced by NGS and analyzed by a metagenomic pipeline, PATHDET.

Results: The putative pathogens were detected by NGS in 5 of 10 FN patients with positive blood culture results, 15 of 87 FN patients (17%) with negative blood culture results, and 3 of 8 NE patients. Several bacteria that were common in the oral, skin, and gut flora were commonly detected in blood samples, suggesting translocation of the human microbiota to the bloodstream in the setting of neutropenia. The cluster analysis of the microbiota in blood samples using NGS demonstrated that the representative bacteria of each cluster were mostly consistent with the pathogens in each patient.

Conclusions: NGS technique has great potential for detecting causative pathogens in patients with FN. Cluster analysis, which extracts characteristic microorganisms from a complex microbial population, may be effective to detect pathogens in minute quantities of microbiota, such as those from the bloodstream.},
}

@article {pmid34859014,
year = {2021},
author = {Cui, Y and Meng, J and Zhang, J and Wang, L and Yan, H and Xia, H and Cao, J and Wu, L},
title = {Case Report: A Case of Sarocladium strictum Meningoencephalitis in an Immunocompetent Patient After Invasive Operation.},
journal = {Frontiers in medicine},
volume = {8},
number = {},
pages = {762763},
pmid = {34859014},
issn = {2296-858X},
abstract = {As an opportunistic phytopathogen, Sarocladium strictum has only been shown to cause neurological disease in immunocompromised patients, where antifungal therapy was not effective. We report a case of Sarocladium strictum meningoencephalitis in an apparently immunocompetent young woman who presented with severe headache and slight fever after undergoing transnasal endoscopic repair of cerebrospinal fluid rhinorrhea. Chronic sinusitis and suspicious intracranial fungal lesions were observed on enhanced magnetic resonance imaging (MRI). Both culture and metagenomic next-generation sequencing of her cerebrospinal fluid were positive for Sarocladium strictum. After local debridement, treatment with amphotericin B plus voriconazole and Ommaya reservoir implantation, the patient improved significantly. Unfortunately, her symptoms worsened again despite plenty of antifungal therapy for a month.},
}

@article {pmid34858931,
year = {2021},
author = {Liu, X and Zhang, Y and Zhang, J and Lou, Z and Xia, H and Lu, Z},
title = {The Early Diagnosis of Scrub Typhus by Metagenomic Next-Generation Sequencing.},
journal = {Frontiers in public health},
volume = {9},
number = {},
pages = {755228},
pmid = {34858931},
issn = {2296-2565},
abstract = {Introduction: Scrub typhus is a mite-borne infection widespread in Southeast Asia, with clinical symptoms such as fever, chills, skin rash, eschar at the bite site, and other signs of acute febrile illness. The Rickettsia pathogen (Orientia tsutsugamushi) is always difficult to be diagnosed at an early stage by traditional clinical diagnostic methods, especially for patients without typical eschar. This greatly increases the mortality of patients with scrub typhus. A new approach should be introduced to improve its clinical diagnosis. Methods: During May 2018 to March 2021, 13 samples from 10 patients with suspected scrub typhus were collected. Metagenomic next-generation sequencing (mNGS) and other diagnostic methods (including serology using Weil-Felix reaction and indirect immunofluorescence test (IIFT) for scrub typhus and respiratory tract profile IgM as well as culture for routine bacteria) were used to identify the pathogens in this study. Results: The results of mNGS were all positive, with mapped reads of O. tsutsugamushi ranging from 1 to 460. Eight patients (80%) were diagnosed as scrub typhus. The other two were diagnosed as suspected scrub typhus due to the limited number of reads of the pathogen (one and two, respectively). According to clinical evidences, nine of the 10 patients were finally diagnosed as scrub typhus, except for patient 9 (suspected scrub typhus by mNGS with one specific reads of the pathogen) diagnosed as acute exacerbation of chronic obstructive pulmonary disease. For the five scrub typhus patients without typical eschar, mNGS gave all positive results (4-460 specific reads). For other methods, only Weil-Felix reaction of one patient detected the pathogen. In addition, the respiratory tract profile (IgM) detected various pathogens, but all were confirmed to be false positive. Conclusions: mNGS performed better than conventional clinical methods to early diagnose scrub typhus. This approach can be routinely carried out for early and precise diagnosis in clinical infections, especially for those hard to be identified by traditional diagnostic methods.},
}

@article {pmid34858369,
year = {2021},
author = {Brüls, T and Baumdicker, F and Smidt, H},
title = {Editorial: Synthetic Microbial Ecology.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {757848},
doi = {10.3389/fmicb.2021.757848},
pmid = {34858369},
issn = {1664-302X},
}

@article {pmid34858042,
year = {2021},
author = {Sohail, MU and Hedin, L and Al-Asmakh, M},
title = {Dysbiosis of the Salivary Microbiome is Associated with Hypertension and Correlated with Metabolic Syndrome Biomarkers.},
journal = {Diabetes, metabolic syndrome and obesity : targets and therapy},
volume = {14},
number = {},
pages = {4641-4653},
pmid = {34858042},
issn = {1178-7007},
abstract = {Background: Hypertension (HT) is an idiopathic disease with severe complications and a high incidence of global mortality. Although the disease shares characteristic features with diabetes and obesity, the complex interplay of endogenous and environmental factors is not well characterized. The oral microbiome has recently been studied to better understand the role of commensal microorganisms in metabolic disorders, including HT, although its role in disease etiology is unclear.

Methods: To bridge this gap, we compared the oral microbiome and clinical chemistry of adult subjects enrolled at Qatar Biobank. Clinical chemistry was performed using Roche Cobas-6000 analyzer. Saliva samples were subjected to 16S rRNA sequencing using Illumina MiSeq platform. Cross-gender comparisons were made between control (males/females) (C-M and C-F) and HT (HT-M and HT-F) groups.

Results: The HT groups had higher (p ≤ 0.05) BMI, plasma glucose, insulin, C-peptide, and alkaline phosphatase (ALP) concentrations. Triglycerides, cholesterol, LDL-cholesterol, and sodium ions were similar among the groups. The microbiome was predominantly occupied by Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Firmicutes were higher (p ≤ 0.05) in the HT groups, whereas Proteobacteria was only higher in the C-F group. Prevotella and Veillonella were significantly higher in the HT groups and exhibited a positive correlation with blood pressure and hyperglycemia. In contrast to other studies, the mathematical summation of priori-select microbes reveals that nitrate-reducing microbes were higher in the HT groups compared with the controls.

Conclusion: In conclusion, these observations suggest a strong association of HT with microbial dysbiosis, where microbial species other than nitrate-reducing microbes contribute to blood pressure regulation. The findings affirm plausible microbial signatures of hypertension and suggest manipulating these microbes as a novel treatment modality. Future experiments are warranted for the mechanistic investigation of hypertension metagenomics and microbial activity.},
}

@article {pmid34857055,
year = {2021},
author = {Aruwa, CE and Pillay, C and Nyaga, MM and Sabiu, S},
title = {Poultry gut health - microbiome functions, environmental impacts, microbiome engineering and advancements in characterization technologies.},
journal = {Journal of animal science and biotechnology},
volume = {12},
number = {1},
pages = {119},
pmid = {34857055},
issn = {1674-9782},
support = {BMGF OPP1180423 2017//Bill and Melinda Gates Foundation/ ; 120433//National Research Foundation South Africa/ ; },
abstract = {The gastrointestinal tract (GIT) health impacts animal productivity. The poultry microbiome has functions which range from protection against pathogens and nutrients production, to host immune system maturation. Fluctuations in the microbiome have also been linked to prevailing environmental conditions. Healthy poultry birds possess a natural resistance to infection. However, the exploration of environmental impacts and other relevant factors on poultry growth and health have been underplayed. Since good performance and growth rate are central to animal production, the host-microbiome relationship remains integral. Prior to the emergence of metagenomic techniques, conventional methods for poultry microbiome studies were used and were low-throughput and associated with insufficient genomic data and high cost of sequencing. Fortunately, the advent of high-throughput sequencing platforms have circumvented some of these shortfalls and paved the way for increased studies on the poultry gut microbiome diversity and functions. Here, we give an up-to-date review on the impact of varied environments on microbiome profile, as well as microbiome engineering and microbiome technology advancements. It is hoped that this paper will provide invaluable information that could guide and inspire further studies on the lingering pertinent questions about the poultry microbiome.},
}

@article {pmid34856894,
year = {2021},
author = {Matsushima, N and Kretsinger, RH},
title = {Novel Sequence Features of Leucine-rich Repeats in Proteins from Nucleo-cytoplasmic Large DNA Viruses.},
journal = {Current protein & peptide science},
volume = {},
number = {},
pages = {},
doi = {10.2174/1389203722666211202151127},
pmid = {34856894},
issn = {1875-5550},
abstract = {Leucine-rich repeats (LRRs) occurring in tandem are 20-29 amino acids long. Eleven LRR types have been recognized. Sequence features of LRRs from viruses were investigated using over 600 LRR proteins from 89 species. Before, metagenome data of nucleo-cytoplasmic large dsDNA viruses (NCLDVs) have been published; the 2,074 NCLDVs encode 199,021 proteins. From the NCLDVs, 549 LRR proteins were identified and analyzed. A comprehensive analysis of TpLRR and FNIP that belong to an LRR class was first performed. The repeating unit lengths (RULs) in five types are 19 residues, which are the shortest among all LRRs. Some RULs are one to five residues shorter than those of the known, corresponding LRR types. The shrinking of RUL is also observed in FNIP. The conserved hydrophobic residues, such as Leu, Val or Ile, in the consensus sequences are frequently substituted by cysteine at one or two positions. Some unique LRR types that are different from those identified previously have been observed. The present study confirms the previous result that the sequence novelty is a general feature of viral LRR proteins.},
}

@article {pmid34856692,
year = {2021},
author = {Li, X and Li, J and Shi, YW and Wu, GD and Wang, MX and Chen, Y and Dong, CM},
title = {[A case report of Streptococcus suis meningoencephalitis diagnosed by metagenomic next-generation sequencing of cerebrospinal fluid and blood].},
journal = {Zhonghua nei ke za zhi},
volume = {60},
number = {12},
pages = {1176-1179},
doi = {10.3760/cma.j.cn112138-20210113-00034},
pmid = {34856692},
issn = {0578-1426},
}

@article {pmid34856283,
year = {2021},
author = {Marcoleta, AE and Arros, P and Varas, MA and Costa, J and Rojas-Salgado, J and Berríos-Pastén, C and Tapia-Fuentes, S and Silva, D and Fierro, J and Canales, N and Chávez, FP and Gaete, A and González, M and Allende, ML and Lagos, R},
title = {The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {152003},
doi = {10.1016/j.scitotenv.2021.152003},
pmid = {34856283},
issn = {1879-1026},
abstract = {The rise of multiresistant bacterial pathogens is currently one of the most critical threats to global health, encouraging a better understanding of the evolution and spread of antimicrobial resistance. In this regard, the role of the environment as a source of resistance mechanisms remains poorly understood. Moreover, we still know a minimal part of the microbial diversity and resistome present in remote and extreme environments, hosting microbes that evolved to resist harsh conditions and thus a potentially rich source of novel resistance genes. This work demonstrated that the Antarctic Peninsula soils host a remarkable microbial diversity and a widespread presence of autochthonous antibiotic-resistant bacteria and resistance genes. We observed resistance to a wide array of antibiotics among isolates, including Pseudomonas resisting ten or more different compounds, with an overall increased resistance in bacteria from non-intervened areas. In addition, genome analysis of selected isolates showed several genes encoding efflux pumps, as well as a lack of known resistance genes for some of the resisted antibiotics, including colistin, suggesting novel uncharacterized mechanisms. By combining metagenomic approaches based on analyzing raw reads, assembled contigs, and metagenome-assembled genomes, we found hundreds of widely distributed genes potentially conferring resistance to different antibiotics (including an outstanding variety of inactivation enzymes), metals, and biocides, hosted mainly by Polaromonas, Pseudomonas, Streptomyces, Variovorax, and Burkholderia. Furthermore, a proportion of these genes were found inside predicted plasmids and other mobile elements, including a putative OXA-like carbapenemase from Polaromonas harboring conserved key residues and predicted structural features. All this evidence indicates that the Antarctic Peninsula soil microbiota has a broad natural resistome, part of which could be transferred horizontally to pathogenic bacteria, acting as a potential source of novel resistance genes.},
}

@article {pmid34855936,
year = {2021},
author = {Yao, J and Gao, J and Guo, J and Wang, H and Zhang, E and Lin, Y and Chen, Z and Li, S and Sun, T},
title = {Characterization of bacteria and antibiotic resistance in commercially-produced cheeses sold in China.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {},
doi = {10.4315/JFP-21-198},
pmid = {34855936},
issn = {1944-9097},
abstract = {The consumption of cheese in China is increasing rapidly. Little is known about the microbiota, the presence of antibiotic-resistant bacteria, or the distribution of antibiotic resistance genes (ARGs) in commercially-produced cheeses sold in China. These are important criteria for evaluating quality and safety. Thus, this study assessed the metagenomics of fifteen types of cheese using 16S rRNA gene sequencing. Fourteen bacterial genera were detected. Lactococcus , Lactobacillus , and Streptococcus were dominant based on numbers of sequence reads. Multidrug-resistant lactic acid bacteria were isolated from most of the types of cheese. The isolates showed 100% and 91.7% resistance to streptomycin and sulfamethoxazole, respectively, and genes involved in acquired resistance to streptomycin (strB) and sulfonamides (sul2) were detected with high frequency. To analyze the distribution of ARGs in the cheeses in overall, 309 ARGs from eight categories of ARG and nine transposase genes were profiled. A total of 169 ARGs were detected in the 15 cheeses; their occurrence and abundance varied significantly between cheeses. Our study demonstrates that there is various diversity of the bacteria and ARGs in cheeses sold in China. The risks associated with multidrug resistance of dominant lactic acid bacteria are of great concern.},
}

@article {pmid34855234,
year = {2021},
author = {Zarei, A and Javid, H and Sanjarian, S and Senemar, S and Zarei, H},
title = {Metagenomics studies for the diagnosis and treatment of prostate cancer.},
journal = {The Prostate},
volume = {},
number = {},
pages = {},
doi = {10.1002/pros.24276},
pmid = {34855234},
issn = {1097-0045},
abstract = {AIM: Mutation occurs in the prostate cell genes, leading to abnormal prostate proliferation and ultimately cancer. Prostate cancer (PC) is one of the most common cancers amongst men, and its prevalence worldwide increases relative to men's age. About 16% of the world's cancers are the result of microbes in the human body. Impaired population balance of symbiosis microbes in the human reproductive system is linked to PC development.

DISCUSSION: With the advent of metagenomics science, the genome sequence of the microbiota of the human body has been unveiled. Therefore, it is now possible to identify a higher range of microbiome changes in PC tissue via the Next Generation Technique, which will have positive consequences in personalized medicine. In this review, we intend to question the role of metagenomics studies in the diagnosis and treatment of PC.

CONCLUSION: The microbial imbalance in the men's genital tract might have an effect on prostate health. Based on next-generation sequencing-generated data, Proteobacteria, Firmicutes, Actinobacteria, and Bacteriodetes are the nine frequent phyla detected in a PC sample, which might be involved in inducing mutation in the prostate cells that cause cancer.},
}

@article {pmid34854758,
year = {2021},
author = {Vilanova, ES and Ramos, A and Oliveira, MCS and Esteves, MB and Gonçalves, MC and Lopes, JRS},
title = {First report of a mastrevirus (Geminiviridae) transmitted by the corn leafhopper.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-09-21-1882-SC},
pmid = {34854758},
issn = {0191-2917},
abstract = {Maize striate mosaic virus (MSMV; genus Mastrevirus), was recently reported in maize plants in Brazil, and also detected by metagenomic analyses in the corn leafhopper, Dalbulus maidis (DeLong & Wolcott). Although these findings suggested that D. maidis is a potential vector, no transmission studies have been performed. Here, we tested the transmission of MSMV by D. maidis from field-collected infected plants and plants infected with MSMV via leafhopper-mediated transmission in the laboratory; all plants were confirmed positive for MSMV by PCR. In each one of three transmission replicates, aviruliferous D. maidis nymphs and adults were confined together on a source plant during a 4-day acquisition access period (AAP), and subsequently transferred to healthy maize seedlings (10 individuals per test plant) in a series of 4-day inoculation access periods (IAPs). We also tested transmission by the corn aphid, Rhopalosiphum maidis (Fitch) and by mechanical inoculation of healthy maize seedlings. Only D. maidis transmitted MSMV, with overall transmission rates of 29.4 and 39.5% using field-collected infected plants, and 18.5% using infected plants in laboratory. D. maidis transmitted MSMV until the third (8-12 days after the AAP) or fourth successive IAP (12-16 days) with gradual loss in transmission efficiency and rate of viruliferous insects over time, suggesting a persistent, but non-propagative mode of transmission. Infected test plants showed mottling symptoms with mild chlorotic streaks and height reduction. This is the first report of transmission of a mastrevirus by D. maidis, facilitating the completion of Koch's postulate for MSMV.},
}

@article {pmid34854727,
year = {2021},
author = {Weil, M and Hoff, KJ and Meißner, W and Schäfer, F and Söllinger, A and Wang, H and Hagenau, L and Kuss, AW and Urich, T},
title = {Full Genome Sequence of a Methanomassiliicoccales Representative Enriched from Peat Soil.},
journal = {Microbiology resource announcements},
volume = {10},
number = {48},
pages = {e0044321},
doi = {10.1128/MRA.00443-21},
pmid = {34854727},
issn = {2576-098X},
support = {ESF/14-BM-A55-0032/16//EC | Emprego, Assuntos Sociais e Inclusão | European Social Fund (ESF)/ ; ESF/14-BM-A55-0013/16//EC | Emprego, Assuntos Sociais e Inclusão | European Social Fund (ESF)/ ; },
abstract = {The full genome of a Methanomassiliicoccales strain, U3.2.1, was obtained from enrichment cultures of percolation fen peat soil under methanogenic conditions, with methanol and hydrogen as the electron acceptor and donor, respectively. Metagenomic assembly of combined long-read and short-read sequences resulted in a 1.51-Mbp circular genome.},
}

@article {pmid34854723,
year = {2021},
author = {Itaya, Y and Nakamura, S and Akiyama, T and Kuninishi, K},
title = {Eukaryotic Communities in Aquatic Mesocosms with and without Calcined Dolomite Investigated Using 18S rRNA Amplicon-Based Metagenomics.},
journal = {Microbiology resource announcements},
volume = {10},
number = {48},
pages = {e0102521},
doi = {10.1128/MRA.01025-21},
pmid = {34854723},
issn = {2576-098X},
abstract = {We report the 18S rRNA gene amplicon data from aquatic mesocosms with and without calcined dolomite. Intramacronucleata and Eumetazoa were present in roughly the same amounts in the water phase in both mesocosms. Chlorophyceae and several groups were detected as the major eukaryotes in the microbes attached to the calcined dolomite surface.},
}

@article {pmid34853518,
year = {2021},
author = {Ma, H and Sun, J and Zhang, L and Liu, Y and Liu, H and Wu, X and Guo, L},
title = {Disseminated Hematogenous Tuberculosis Following in vitro Fertilization-Embryo Transfer: A Case Report.},
journal = {Infection and drug resistance},
volume = {14},
number = {},
pages = {4903-4911},
doi = {10.2147/IDR.S332992},
pmid = {34853518},
issn = {1178-6973},
abstract = {This study aimed to analyze the diagnosis and treatment process of patients with hematogenous disseminated pulmonary tuberculosis after treatment with in vitro fertilization-embryo transfer (IVF-ET). We retrospectively analyzed the clinical data, including imaging and etiological data, the use of antimicrobials, metagenomic next-generation sequencing (mNGS) results, and the treatment process, of a patient who underwent IVF-ET due to an obstruction in the fallopian tube; after the treatment, she developed a persistent fever with shortness of breath and suffered a spontaneous abortion. Due to the failure of other treatment modalities, fiber optic bronchoscopy was performed, and the alveolar lavage fluid was obtained for mNGS. Tests for Mycobacterium tuberculosis and rifampicin resistance (Xpert MTB/RIF) showed positive and negative results, respectively. Subsequently, anti-tuberculosis treatment with isoniazid, rifampicin, pyrazinamide, and ethambutol was administered. After the patient's condition improved, she was transferred to a specialized tuberculosis hospital for further treatment, where she died one month later from multiple organ failure. From this case, we conclude that clinicians should remain highly vigilant for pulmonary infection with M. tuberculosis in pregnant women, particularly in patients treated with IVF-ET, and check for its presence as soon as possible.},
}

@article {pmid34853367,
year = {2021},
author = {Thaduri, S and Marupakula, S and Terenius, O and Onorati, P and Tellgren-Roth, C and Locke, B and de Miranda, JR},
title = {Global similarity, and some key differences, in the metagenomes of Swedish varroa-surviving and varroa-susceptible honeybees.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {23214},
pmid = {34853367},
issn = {2045-2322},
support = {2013-1225//Svenska Forskningsrådet Formas/ ; 2013-1225//Svenska Forskningsrådet Formas/ ; 3.2.18-5045/15//Nationella Honungsprogrammet/ ; },
abstract = {There is increasing evidence that honeybees (Apis mellifera L.) can adapt naturally to survive Varroa destructor, the primary cause of colony mortality world-wide. Most of the adaptive traits of naturally varroa-surviving honeybees concern varroa reproduction. Here we investigate whether factors in the honeybee metagenome also contribute to this survival. The quantitative and qualitative composition of the bacterial and viral metagenome fluctuated greatly during the active season, but with little overall difference between varroa-surviving and varroa-susceptible colonies. The main exceptions were Bartonella apis and sacbrood virus, particularly during early spring and autumn. Bombella apis was also strongly associated with early and late season, though equally for all colonies. All three affect colony protein management and metabolism. Lake Sinai virus was more abundant in varroa-surviving colonies during the summer. Lake Sinai virus and deformed wing virus also showed a tendency towards seasonal genetic change, but without any distinction between varroa-surviving and varroa-susceptible colonies. Whether the changes in these taxa contribute to survival or reflect demographic differences between the colonies (or both) remains unclear.},
}

@article {pmid34852632,
year = {2021},
author = {Wang, C and Yang, Q and Liu, N and Huang, R and Fang, M and Shao, M},
title = {Emphysematous gastritis associated with mucormycosis in a patient with fulminant myocarditis requiring veno-arterial extracorporeal membrane oxygenation.},
journal = {Revista espanola de enfermedades digestivas : organo oficial de la Sociedad Espanola de Patologia Digestiva},
volume = {},
number = {},
pages = {},
doi = {10.17235/reed.2021.8477/2021},
pmid = {34852632},
issn = {1130-0108},
abstract = {We present the case of a 37-year-old male who admitted to our hospital with fever, weakness, limb pain for 6 days and dyspnea for 14 hours .The patient had no immune related diseases.He was rapidly diagnosed with fulminant myocarditis and progressed to severe cardiogenic shock during the early stage.Then he was treated with V-A extracorporeal membrane oxygenation (ECMO). It is worth mentioning that the patient's peripheral blood was taken for metagenomic Next-Generation Sequencing(mNGS) upon admission and the results did not find any pathogenic bacteria.But there is no further examination(such as coronary angiography and myocardial biopsy) to determine the etiology of myocarditis.},
}

@article {pmid34852245,
year = {2021},
author = {Yin, M and Zheng, Y and Zhang, L and Qin, W and Han, H and Wu, D and Wang, H},
title = {The real-life performance of metagenomic next-generation sequencing in sepsis.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jinf.2021.11.018},
pmid = {34852245},
issn = {1532-2742},
}

@article {pmid34851722,
year = {2021},
author = {Zheng, B and He, Y and Zhang, P and Huo, YX and Yin, Y},
title = {Polyphenol utilization proteins in human gut microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {AEM0185121},
doi = {10.1128/AEM.01851-21},
pmid = {34851722},
issn = {1098-5336},
abstract = {Dietary polyphenols can significantly benefit human health, but their bioavailability is metabolically controlled by human gut microbiota. To facilitate the study of polyphenol metabolism for human gut health, we have manually curated experimentally characterized polyphenol utilization proteins (PUPs) from published literature. This resulted in 60 experimentally characterized PUPs (named seeds) with various metadata, such as species and substrate. Further database search found 107,851 homologs of the seeds from UniProt and UHGP (Unified Human Gastrointestinal Protein) databases. All PUP seeds and homologs were classified into protein classes, families and subfamilies based on Enzyme Commission (EC) numbers, Pfam (protein family) domains and sequence similarity networks. By locating PUP homologs in the genomes of UHGP, we have identified 1,074 physically linked PUP gene clusters (PGCs), which are potentially involved in polyphenol metabolism in the human gut. The gut microbiome of Africans was consistently ranked the top in terms of the abundance and prevalence of PUP homologs and PGCs among all geographical continents. This reflects the fact that dietary polyphenols are more commonly consumed by African population than other populations such as Europeans and North Americans. A case study of the Hadza hunter-gatherer microbiome verified the feasibility of using dbPUP to profile metagenomic data for biologically meaningful discovery, suggesting an association between diet and PUP abundance. A Pfam domain enrichment analysis of PGCs identified a number of putatively novel PUP families. Lastly, a user-friendly web interface (https://bcb.unl.edu/dbpup/) provides all the data online to facilitate the research of polyphenol metabolism for improved human health. Importance Long-term consumption of polyphenol-rich foods have been shown to lower the risk of various human diseases such as cardiovascular diseases, cancers, and metabolic diseases. Raw polyphenols are often enzymatically processed by gut microbiome, which encode various polyphenol utilization proteins (PUPs) to produce metabolites with much higher bioaccessibility to gastrointestinal cells. This study delivered dbPUP as an online database for experimentally characterized PUPs and their homologs in human gut microbiome. This work also performed a systematic classification of PUPs into enzyme classes, families, and subfamilies. The signature Pfam domains were identified for PUP families, enabling conserved domain-based PUP annotation. This standardized sequence similarity-based PUP classification system offered a guideline for the future inclusion of new experimentally characterized PUPs and the creation of new PUP families. An in-depth data analysis was further conducted on PUP homologs and physically linked PUP gene clusters (PGCs) in gut microbiomes of different human populations.},
}

@article {pmid34851441,
year = {2021},
author = {Oh, HN and Myeong, NR and Kim, T and Min, GS and Kim, S and Sul, WJ},
title = {Changes in Fecal Pellet Microbiome of the Cold-Adapted Antarctic Copepod Tigriopus kingsejongensis at Different Temperatures and Developmental Stages.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {34851441},
issn = {1432-184X},
support = {Graduate Research Scholarship in 2016//Chung-Ang University/ ; NRF-2019R1A2C1090861//National Research Foundation of Korea/ ; PE21140//Korea Polar Research Institute/ ; },
abstract = {Tigriopus kingsejongensis, a copepod species reported from the King Sejong Station, Antarctica, serves as a valuable food resource in ecosystems. We cultured T. kingsejongensis at three different temperatures (2 °C, 8 °C, and 15 °C) in a laboratory to observe the changes in its fecal pellet microbiome depending on the cultivation temperatures and developmental stages. We observed that the fecal pellet microbiome of the copepod changed with temperature: a lower microbial diversity, higher abundance of the aquatic bacterium Vibrio, and lower abundance of the psychrophilic bacterium Colwellia were noted at higher temperatures. In addition, the fecal pellet microbiome of the copepod changed according to the developmental stage: a lower microbial diversity was noted in egg-attached copepods than in nauplii at 8 °C. We further analyzed three shotgun metagenomes from the fecal pellet samples of T. kingsejongensis at different temperatures and obtained 44 metagenome-assembled genomes (MAGs). We noted that MAGs of V. splendidus D contained glycosyl hydrolases (GHs) encoding chitinases and virulence factors at a higher relative abundance at 15 °C than at lower temperatures. These results indicate that increasing temperature affects the fecal pellet microbiome and the development of copepods. The findings are helpful to understand the changes in cold-adapted copepods and the effect of temperature on their growth.},
}

@article {pmid34851181,
year = {2021},
author = {Wu, K and Xu, Y and Zhang, W and Mao, H and Chen, B and Zheng, Y and Hu, X},
title = {Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191821},
doi = {10.1128/Spectrum.01918-21},
pmid = {34851181},
issn = {2165-0497},
abstract = {This study aimed to compare the fecal microbiome and antimicrobial resistance between captive and free-range sika deer with the same exposure to antibiotic anthelmintics. The taxonomic differences mainly involved significant changes in the dominant phyla, genera, and species. Linear discriminant analysis effect size (LEfSe) analysis revealed that 22 taxa were significantly different between the two groups. The KEGG analysis showed that the fecal microbiome metabolic function, and all level 2 categories in metabolism had higher abundance in the free-range deer. Based on the carbohydrate-active enzyme (CAZy) database analysis, glycoside hydrolases and carbohydrate-binding modules showed remarkable differences between the two groups. Regarding antibiotic resistance, tetQ and lnuC dominated the antibiotic resistance ontology (ARO) terms, and tetracycline and lincosamide resistance dominated the antimicrobial resistance patterns. Furthermore, the lnuC, ErmF, and tetW/N/W AROs and lincosamide resistance showed higher abundance in the captive deer, suggesting that captivity may yield more serious resistance issues because of the differences in greenfeed diet, breeding density, and/or housing environment. The results also revealed important associations between the phylum Proteobacteria, genus Prevotella, and major antibiotic resistance genes. Although the present study was a pilot study with a limited sample size that was insufficient control for some potential factors, it serves as the metagenomic study on the microbial communities and antimicrobial resistance in sika deer. IMPORTANCE We used a metagenomic approach to investigate whether and how captive and free-range impact the microbial communities and antimicrobial resistance in sika deer. The results provide solid evidence of the significant impacts on the microbial composition and function in captive and free-range sika deer. Interestingly, although the sika deer had the same exposure to antibiotic anthelmintics, the antimicrobial resistances were affected by the breeding environment.},
}

@article {pmid34851164,
year = {2021},
author = {Murray, AE and Lo, CC and Daligault, HE and Avalon, NE and Read, RW and Davenport, KW and Higham, ML and Kunde, Y and Dichosa, AEK and Baker, BJ and Chain, PSG},
title = {Discovery of an Antarctic Ascidian-Associated Uncultivated Verrucomicrobia with Antimelanoma Palmerolide Biosynthetic Potential.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0075921},
doi = {10.1128/mSphere.00759-21},
pmid = {34851164},
issn = {2379-5042},
abstract = {The Antarctic marine ecosystem harbors a wealth of biological and chemical innovation that has risen in concert over millennia since the isolation of the continent and formation of the Antarctic circumpolar current. Scientific inquiry into the novelty of marine natural products produced by Antarctic benthic invertebrates led to the discovery of a bioactive macrolide, palmerolide A, that has specific activity against melanoma and holds considerable promise as an anticancer therapeutic. While this compound was isolated from the Antarctic ascidian Synoicum adareanum, its biosynthesis has since been hypothesized to be microbially mediated, given structural similarities to microbially produced hybrid nonribosomal peptide-polyketide macrolides. Here, we describe a metagenome-enabled investigation aimed at identifying the biosynthetic gene cluster (BGC) and palmerolide A-producing organism. A 74-kbp candidate BGC encoding the multimodular enzymatic machinery (hybrid type I-trans-AT polyketide synthase-nonribosomal peptide synthetase and tailoring functional domains) was identified and found to harbor key features predicted as necessary for palmerolide A biosynthesis. Surveys of ascidian microbiome samples targeting the candidate BGC revealed a high correlation between palmerolide gene targets and a single 16S rRNA gene variant (R = 0.83 to 0.99). Through repeated rounds of metagenome sequencing followed by binning contigs into metagenome-assembled genomes, we were able to retrieve a nearly complete genome (10 contigs) of the BGC-producing organism, a novel verrucomicrobium within the Opitutaceae family that we propose here as "Candidatus Synoicihabitans palmerolidicus." The refined genome assembly harbors five highly similar BGC copies, along with structural and functional features that shed light on the host-associated nature of this unique bacterium. IMPORTANCE Palmerolide A has potential as a chemotherapeutic agent to target melanoma. We interrogated the microbiome of the Antarctic ascidian, Synoicum adareanum, using a cultivation-independent high-throughput sequencing and bioinformatic strategy. The metagenome-encoded biosynthetic machinery predicted to produce palmerolide A was found to be associated with the genome of a member of the S. adareanum core microbiome. Phylogenomic analysis suggests the organism represents a new deeply branching genus, "Candidatus Synoicihabitans palmerolidicus," in the Opitutaceae family of the Verrucomicrobia phylum. The Ca. Synoicihabitans palmerolidicus 4.29-Mb genome encodes a repertoire of carbohydrate-utilizing and transport pathways, a chemotaxis system, flagellar biosynthetic capacity, and other regulatory elements enabling its ascidian-associated lifestyle. The palmerolide producer's genome also contains five distinct copies of the large palmerolide biosynthetic gene cluster that may provide structural complexity of palmerolide variants.},
}

@article {pmid34850947,
year = {2021},
author = {Liu, B and Zheng, D and Zhou, S and Chen, L and Yang, J},
title = {VFDB 2022: a general classification scheme for bacterial virulence factors.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkab1107},
pmid = {34850947},
issn = {1362-4962},
support = {31970635//National Natural Science Foundation of China/ ; 2017-I2M-3-017//CAMS Innovation Fund for Medical Sciences/ ; //National Scientific Data Sharing Platform for Population and Health/ ; },
abstract = {The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to presenting a comprehensive knowledge base and a versatile analysis platform for bacterial virulence factors (VFs). Recent developments in sequencing technologies have led to increasing demands to analyze potential VFs within microbiome data that always consist of many different bacteria. Nevertheless, the current classification of VFs from various pathogens is based on different schemes, which create a chaotic situation and form a barrier for the easy application of the VFDB dataset for future panbacterial metagenomic analyses. Therefore, based on extensive literature mining, we recently proposed a general category of bacterial VFs in the database and reorganized the VFDB dataset accordingly. Thus, all known bacterial VFs from 32 genera of common bacterial pathogens collected in the VFDB are well grouped into 14 basal categories along with over 100 subcategories in a hierarchical architecture. The new coherent and well-defined VFDB dataset will be feasible and applicable for future panbacterial analysis in terms of virulence factors. In addition, we introduced a redesigned JavaScript-independent web interface for the VFDB website to make the database readily accessible to all users with various client settings worldwide.},
}

@article {pmid34850410,
year = {2021},
author = {Dike, KS and Okafor, CP and Ohabuhiro, BN and Maduwuba, MC and Ezeokoli, OT and Ayeni, KI and Okafor, CM and Ezekiel, CN},
title = {Analysis of Bacterial Communities of Three Cassava-Based Traditionally Fermented Nigerian Foods (abacha, fufu and garri).},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/lam.13621},
pmid = {34850410},
issn = {1472-765X},
abstract = {Globally, cassava is an important food crop that contributes significantly to food security. In Nigeria, cassava can be traditionally processed into abacha (fermented strips), fufu (submerged-fermented porridge) and garri (solid-state fermented farinated granules) for human consumption. Despite the widespread consumption of these foods, there is a major knowledge gap in understanding their core bacterial diversity. This study, therefore, applied next-generation sequencing of 16S rRNA gene to delineate the bacterial diversity in abacha, fufu and garri. Amplicon sequence variants belonging to nine phyla were present in the three foods. Firmicutes dominated the bacterial community of abacha and fufu, whereas, Proteobacteria was the dominant phylum in garri. At genus level taxa, Lactococcus, Lysinibacillus and Pseudomonas dominated the bacterial community in abacha, fufu and garri, respectively. Other dominant phylotypes reported in the foods belonged to Bacillus, Clostridium sensu stricto (cluster 1), Cupriavidus, Enterobacter, Sphingomonas and Staphylococcus. To the best of our knowledge, Clostridium sensu stricto cluster 1 and Lysinibacillus in fufu, and Brevundimonas, Cupriavidus, Sphingomonas and Strenotrophomomas in garri are reported for the first time. Although some potential pathogenic genera were recorded, the foods contained potentially functional species that could be explored to improve artisanal food production, food security and safeguard consumer health.},
}

@article {pmid34850388,
year = {2021},
author = {Chegu Krishnamurthi, M and Sarada, R and Mudliar, SN},
title = {Unravelling of Chlorella associated bacterial load, diversity, and their imputed functions at high and low yield conditions through metagenome sequencing.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.13225},
pmid = {34850388},
issn = {1529-8817},
abstract = {Chlorella-associated bacteria can have a significant influence on facilitating higher Chlorella biomass yield due to their symbiotic relationship. In this study, non-axenic Chlorella was cultivated in an airlift photobioreactor at high and low-yield conditions. The associated bacterial diversity was analyzed using 16S rRNA metagenome sequencing. At high yield conditions, the bacterial load was observed in the range of 108 -1010 CFU/mL, whereas at low yield conditions, bacteria were more dominant and observed in the range of 1014 -1015 CFU · mL-1 . The majority of the bacterial species associated with Chlorella at high yield conditions belongs to Proteobacteria, Bacteroidetes. Further, Bacteroidetes levels were decreased at low yield conditions and were highly diversified with Planctomycetes, Firmicutes, and 18 others. Predicted functional genes indicated that Chlorella-associated bacteria have the enzymes involved in the metabolism and biosynthesis of B-complex vitamins (i.e., vitamin B12 , thiamin, biotin, pyridoxine, and riboflavin). A critical evaluation revealed that vitamin biosynthesis genes were more abundant at low yield conditions, however, vitamin B12 transport genes (B12 transport ATP binding protein, B12 substrate-binding transportation, B12 permease protein) were less abundant, indicating even though vitamins production occurs, but their availability to Chlorella was limited due to the lack of vitamin transport genes. Further, at high yield, Chlorella-associated bacteria enabled higher growth by supplementing the vitamins. In contrast, at low yield condition - an increased bacterial load, diversity, and limited vitamin transport functional genes affected the Chlorella yield. It can be inferred that Chlorella yield was significantly affected by three factors: associated bacterial load, diversity, and transport functional genes of vitamins.},
}

@article {pmid34850155,
year = {2021},
author = {Jhong, JH and Yao, L and Pang, Y and Li, Z and Chung, CR and Wang, R and Li, S and Li, W and Luo, M and Ma, R and Huang, Y and Zhu, X and Zhang, J and Feng, H and Cheng, Q and Wang, C and Xi, K and Wu, LC and Chang, TH and Horng, JT and Zhu, L and Chiang, YC and Wang, Z and Lee, TY},
title = {dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkab1080},
pmid = {34850155},
issn = {1362-4962},
support = {32070659//National Natural Science Foundation of China/ ; 2021A1515012447//Guangdong Province Basic and Applied Basic Research Fund/ ; 2021E007//Ganghong Young Scholar Development Fund/ ; JCYJ20200109150003938//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; P2-2021-ZYL-001-A//Chinese University of Hong Kong/ ; },
abstract = {The last 18 months, or more, have seen a profound shift in our global experience, with many of us navigating a once-in-100-year pandemic. To date, COVID-19 remains a life-threatening pandemic with little to no targeted therapeutic recourse. The discovery of novel antiviral agents, such as vaccines and drugs, can provide therapeutic solutions to save human beings from severe infections; however, there is no specifically effective antiviral treatment confirmed for now. Thus, great attention has been paid to the use of natural or artificial antimicrobial peptides (AMPs) as these compounds are widely regarded as promising solutions for the treatment of harmful microorganisms. Given the biological significance of AMPs, it was obvious that there was a significant need for a single platform for identifying and engaging with AMP data. This led to the creation of the dbAMP platform that provides comprehensive information about AMPs and facilitates their investigation and analysis. To date, the dbAMP has accumulated 26 447 AMPs and 2262 antimicrobial proteins from 3044 organisms using both database integration and manual curation of >4579 articles. In addition, dbAMP facilitates the evaluation of AMP structures using I-TASSER for automated protein structure prediction and structure-based functional annotation, providing predictive structure information for clinical drug development. Next-generation sequencing (NGS) and third-generation sequencing have been applied to generate large-scale sequencing reads from various environments, enabling greatly improved analysis of genome structure. In this update, we launch an efficient online tool that can effectively identify AMPs from genome/metagenome and proteome data of all species in a short period. In conclusion, these improvements promote the dbAMP as one of the most abundant and comprehensively annotated resources for AMPs. The updated dbAMP is now freely accessible at http://awi.cuhk.edu.cn/dbAMP.},
}

@article {pmid34850116,
year = {2021},
author = {Schmartz, GP and Hartung, A and Hirsch, P and Kern, F and Fehlmann, T and Müller, R and Keller, A},
title = {PLSDB: advancing a comprehensive database of bacterial plasmids.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkab1111},
pmid = {34850116},
issn = {1362-4962},
support = {//Saarland University/ ; //Helmholtz-Institute for Pharmaceutical Research Saarland/ ; },
abstract = {Plasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity and scale of metagenomics experiments, the number of reported plasmids is rapidly growing as well, amassing a considerable number of false positives due to undetected misassembles. Here, our previously published database PLSDB provides a reliable resource for researchers to quickly compare their sequences against selected and annotated previous findings. Within two years, the size of this resource has more than doubled from the initial 13,789 to now 34,513 entries over the course of eight regular data updates. For this update, we aggregated community feedback for major changes to the database featuring new analysis functionality as well as performance, quality, and accessibility improvements. New filtering steps, annotations, and preprocessing of existing records improve the quality of the provided data. Additionally, new features implemented in the web-server ease user interaction and allow for a deeper understanding of custom uploaded sequences, by visualizing similarity information. Lastly, an application programming interface was implemented along with a python library, to allow remote database queries in automated workflows. The latest release of PLSDB is freely accessible under https://www.ccb.uni-saarland.de/plsdb.},
}

@article {pmid34849793,
year = {2021},
author = {Mercurio, K and Singh, D and Walden, E and Baetz, K},
title = {Global analysis of Saccharomyces cerevisiae growth in mucin.},
journal = {G3 (Bethesda, Md.)},
volume = {11},
number = {11},
pages = {},
doi = {10.1093/g3journal/jkab294},
pmid = {34849793},
issn = {2160-1836},
support = {RGPIN-2019-06164//Natural Sciences and Engineering Council of Canada/ ; //NSERC Collaborative Research and Training Program/ ; //NSERC Postgraduate Scholarships-Doctoral Program/ ; },
abstract = {Metagenomic profiling of the human gut microbiome has discovered DNA from dietary yeasts like Saccharomyces cerevisiae. However, it is unknown if the S. cerevisiae detected by common metagenomic methods are from dead dietary sources, or from live S. cerevisiae colonizing the gut similar to their close relative Candida albicans. While S. cerevisiae can adapt to minimal oxygen and acidic environments, it has not been explored whether this yeast can metabolize mucin, the large, gel-forming, highly glycosylated proteins representing a major source of carbon in the gut mucosa. We reveal that S. cerevisiae can utilize mucin as their main carbon source, as well as perform both a transcriptome analysis and a chemogenomic screen to identify biological pathways required for this yeast to grow optimally in mucin. In total, 739 genes demonstrate significant differential expression in mucin culture, and deletion of 21 genes impact growth in mucin. Both screens suggest that mitochondrial function is required for proper growth in mucin, and through secondary assays we determine that mucin exposure induces mitogenesis and cellular respiration. We further show that deletion of an uncharacterized ORF, YCR095W-A, led to dysfunction in mitochondrial morphology and oxygen consumption in mucin. Finally, we demonstrate that Yps7, an aspartyl protease and homolog to mucin-degrading proteins in C. albicans, is important for growth on mucin. Collectively, our work serves as the initial step toward establishing how this common dietary fungus can survive in the mucus environment of the human gut.},
}

@article {pmid34849595,
year = {2021},
author = {Tang, D and Li, Y and Tan, D and Fu, J and Tang, Y and Lin, J and Zhao, R and Du, H and Zhao, Z},
title = {KCOSS: an ultra-fast k-mer counter for assembled genome analysis.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btab797},
pmid = {34849595},
issn = {1367-4811},
abstract = {MOTIVATION: The k-mer frequency in whole genome sequences provides researchers with an insightful perspective on genomic complexity, comparative genomics, metagenomics, and phylogeny. The current k-mer counting tools are typically slow, and they require large memory and hard disk for assembled genome analysis.

RESULTS: We propose a novel and ultra-fast k-mer counting algorithm, KCOSS, to fulfill k-mer counting mainly for assembled genomes with segmented Bloom filter, lock-free queue, lock-free thread pool, and cuckoo hash table. We optimize running time and memory consumption by recycling memory blocks, merging multiple consecutive first-occurrence k-mers into C-read, and writing a set of C-reads to disk asynchronously. KCOSS was comparatively tested with Jellyfish2, CHTKC, and KMC3 on seven assembled genomes and three sequencing datasets in running time, memory consumption, and hard disk occupation. The experimental results show that KCOSS counts k-mer with less memory and disk while having a shorter running time on assembled genomes. KCOSS can be used to calculate the k-mer frequency not only for assembled genomes but also for sequencing data.

AVAILABILITY: The KCOSS software is implemented in C ++. It is freely available on GitHub: https://github.com/kcoss-2021/KCOSS.

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

@article {pmid34849195,
year = {2021},
author = {Garcia, BJ and Simha, R and Garvin, M and Furches, A and Jones, P and Gazolla, JGFM and Hyatt, PD and Schadt, CW and Pelletier, D and Jacobson, D},
title = {A k-mer based approach for classifying viruses without taxonomy identifies viral associations in human autism and plant microbiomes.},
journal = {Computational and structural biotechnology journal},
volume = {19},
number = {},
pages = {5911-5919},
doi = {10.1016/j.csbj.2021.10.029},
pmid = {34849195},
issn = {2001-0370},
abstract = {Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an essential role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus' genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples, even if they do not have a taxonomy. To identify and quantify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses to create a database of metagenomic viruses. The resulting Kraken2 database of the metagenomic viruses can be found here: https://www.osti.gov/biblio/1615774 and is compatible with Kraken2. We then integrated the viral classification database with databases created with genomes from NCBI for use with ParaKraken (a parallelized version of Kraken provided in Supplemental Zip 1), a metagenomic/transcriptomic classifier. To illustrate the breadth of our utility for classifying metagenome viruses, we analyzed data from a plant metagenome study identifying genotypic and compartment specific differences between two Populus genotypes in three different compartments. We also identified a significant increase in abundance of eight viral sequences in post mortem brains in a human metatranscriptome study comparing Autism Spectrum Disorder patients and controls. We also show the potential accuracy for classifying viruses by utilizing both the JGI and NCBI viral databases to identify the uniqueness of viral sequences. Finally, we validate the accuracy of viral classification with NCBI databases containing viruses with taxonomy to identify pathogenic viruses in known COVID-19 and cassava brown streak virus infection samples. Our method represents the compulsory first step in better understanding the role of viruses in the microbiome by allowing for a more complete identification of sequences without taxonomy. Better classification of viruses will improve identifying associations between viruses and their hosts as well as viruses and other microbiome members. Despite the lack of taxonomy, this database of metagenomic viruses can be used with any tool that utilizes a taxonomy, such as Kraken, for accurate classification of viruses.},
}

@article {pmid34847392,
year = {2021},
author = {Yin, X and Yang, Y and Deng, Y and Huang, Y and Li, L and Chan, LYL and Zhang, T},
title = {An assessment of resistome and mobilome in wastewater treatment plants through temporal and spatial metagenomic analysis.},
journal = {Water research},
volume = {209},
number = {},
pages = {117885},
doi = {10.1016/j.watres.2021.117885},
pmid = {34847392},
issn = {1879-2448},
abstract = {Wastewater treatment plants (WWTPs) are regarded as critical points in disseminating antibiotic resistance genes (ARGs). In particular, the discharging effluents from WWTPs generally bring downstream catchment areas exogenous ARGs and resistant bacteria. However, there lacks a sufficient assessment of the resistome and mobilome in effluents. In this study, a consecutive monthly sampling was conducted over 13 months in three Hong Kong (HK) WWTPs for metagenomic sequencing. Prevalence information of ARGs and mobile genetic elements (MGEs) was compared with counterparts in effluents from cities of North America, South America, Europe, and Asia. Moreover, a publicly accessible platform integrating the exposure ranking scheme, which was based on the global archive of ARG abundance, and a readily implementable online pipeline was developed to benefit communication in academia and government consultancy. Results demonstrated HK WWTPs were featured high ARG removal efficiency of 2.34-2.43 log reduction rate, and effluents were ranked in moderate levels of Level 2 and Level 3 in the exposure prioritizing scheme based on total ARG abundance. Moreover, absolute quantification of temporal variations of effluent resistome disclosed distinct changes over time among varied ARG types which were associated with prevalently used antibiotics, including quinolone and sulfonamide. This reinforces the need for real-time management of WWTP systems. Notably, ARGs of anthropogenic prevalence, high mobility, and potential pathogenicity were found to be present in HK effluents, drawing attention to the necessity for improved risk management. In addition, source tracking of effluent resistome and structural equation model analysis was conducted to explore the disparity in ARG abundance and diversity in different samples. The discovery of this study and the recommendation of a comprehensive exposure assessment will facilitate decision-making in resistome management in WWTPs to reduce the ARG and antibiotic resistant bacteria (ARB) contamination in the receiving environments.},
}

@article {pmid34847370,
year = {2021},
author = {Wang, D and Doestzada, M and Chen, L and Andreu-Sánchez, S and van den Munckhof, ICL and Augustijn, HE and Koehorst, M and Ruiz-Moreno, AJ and Bloks, VW and Riksen, NP and Rutten, JHW and Joosten, LAB and Netea, MG and Wijmenga, C and Zhernakova, A and Kuipers, F and Fu, J},
title = {Characterization of gut microbial structural variations as determinants of human bile acid metabolism.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2021.11.003},
pmid = {34847370},
issn = {1934-6069},
abstract = {Bile acids (BAs) facilitate intestinal fat absorption and act as important signaling molecules in host-gut microbiota crosstalk. BA-metabolizing pathways in the microbial community have been identified, but it remains largely unknown how the highly variable genomes of gut bacteria interact with host BA metabolism. We characterized 8,282 structural variants (SVs) of 55 bacterial species in the gut microbiomes of 1,437 individuals from two cohorts and performed a systematic association study with 39 plasma BA parameters. Both variations in SV-based continuous genetic makeup and discrete clusters showed correlations with BA metabolism. Metagenome-wide association analysis identified 809 replicable associations between bacterial SVs and BAs and SV regulators that mediate the effects of lifestyle factors on BA metabolism. This is the largest microbial genetic association analysis to demonstrate the impact of bacterial SVs on human BA composition, and it highlights the potential of targeting gut microbiota to regulate BA metabolism through lifestyle intervention.},
}

@article {pmid34847216,
year = {2021},
author = {Sirven, MA and Venancio, VP and Shankar, S and Klemashevich, C and Castellón-Chicas, MJ and Fang, C and Mertens-Talcott, SU and Talcott, ST},
title = {Ulcerative colitis results in differential metabolism of cranberry polyphenols by the colon microbiome in vitro.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d1fo03047g},
pmid = {34847216},
issn = {2042-650X},
abstract = {The microbiome plays a major role in polyphenol metabolism, producing metabolites that are bioavailable and potentially more bioactive than the compounds from which they are derived. However, the microbiome can vary among individuals, and especially for those with co-morbidities, such as ulcerative colitis. In subjects with ulcerative colitis, the consequence of a 'dysbiotic' microbiome is characterized by decreased diversity of microbiota that may impact their capability to metabolize polyphenols into bioavailable metabolites. On this premise, the microbiome metabolism of cranberry polyphenols between healthy individuals and those with ulcerative colitis was compared in vitro. Fecal samples from volunteers, with or without diagnosed ulcerative colitis, were cultured anaerobically in the presence of cranberry polyphenols. The resulting metabolites were then quantified via LC-ESI-MS/MS. 16S rRNA metagenomics analysis was also utilized to assess differences in microbiota composition between healthy and ulcerative colitis microbiomes and the modulatory effects of cranberry polyphenols on microbiota composition. Healthy microbiomes produced higher (p < 0.05) concentrations of 5-(3',4'-dihydroxyphenyl)-gamma-valerolactone and 3-hydroxyphenylacetic acid in comparison to ulcerative colitis microbiomes. Additionally, healthy microbiomes contained a higher (p < 0.05) abundance of Ruminococcaceae, which could explain their ability to produce higher concentrations of cranberry polyphenol metabolites. Health status and the presence of cranberry polyphenols also significantly impacted the production of several short-chain and branched-chain fatty acids. These results suggest that efficiency of polyphenol metabolism is dependent on microbiota composition and future works should include metabolite data to account for inter-individual differences in polyphenol metabolism.},
}

@article {pmid34846288,
year = {2021},
author = {van der Graaf-van Bloois, L and Wagenaar, JA and Zomer, AL},
title = {RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning.},
journal = {Microbial genomics},
volume = {7},
number = {11},
pages = {},
doi = {10.1099/mgen.0.000683},
pmid = {34846288},
issn = {2057-5858},
abstract = {Antimicrobial-resistance (AMR) genes in bacteria are often carried on plasmids and these plasmids can transfer AMR genes between bacteria. For molecular epidemiology purposes and risk assessment, it is important to know whether the genes are located on highly transferable plasmids or in the more stable chromosomes. However, draft whole-genome sequences are fragmented, making it difficult to discriminate plasmid and chromosomal contigs. Current methods that predict plasmid sequences from draft genome sequences rely on single features, like k-mer composition, circularity of the DNA molecule, copy number or sequence identity to plasmid replication genes, all of which have their drawbacks, especially when faced with large single-copy plasmids, which often carry resistance genes. With our newly developed prediction tool RFPlasmid, we use a combination of multiple features, including k-mer composition and databases with plasmid and chromosomal marker proteins, to predict whether the likely source of a contig is plasmid or chromosomal. The tool RFPlasmid supports models for 17 different bacterial taxa, including Campylobacter, Escherichia coli and Salmonella, and has a taxon agnostic model for metagenomic assemblies or unsupported organisms. RFPlasmid is available both as a standalone tool and via a web interface.},
}

@article {pmid34846173,
year = {2021},
author = {Aylward, J and Wingfield, MJ and Roets, F and Wingfield, BD},
title = {A high-quality fungal genome assembly resolved from a sample accidentally contaminated by multiple taxa.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {},
doi = {10.2144/btn-2021-0097},
pmid = {34846173},
issn = {1940-9818},
support = {//Tree Protection Co-operative Program (TPCP)/ ; //SARChI chair in Fungal Genomics/ ; //Department of Science and Technology (DST)-National Research Foundation (NRF) Centre of Excellence in Plant Health Biotechnology (CPHB)/ ; },
abstract = {Contamination in sequenced genomes is a relatively common problem and several methods to remove non-target sequences have been devised. Typically, the target and contaminating organisms reside in different kingdoms, simplifying their separation. The authors present the case of a genome for the ascomycete fungus Teratosphaeria eucalypti, contaminated by another ascomycete fungus and a bacterium. Approaching the problem as a low-complexity metagenomics project, the authors used two available software programs, BlobToolKit and anvi'o, to filter the contaminated genome. Both the de novo and reference-assisted approaches yielded a high-quality draft genome assembly for the target fungus. Incorporating reference sequences increased assembly completeness and visualization elucidated previously unknown genome features. The authors suggest that visualization should be routine in any sequencing project, regardless of suspected contamination.},
}

@article {pmid34845701,
year = {2022},
author = {Raza, A and Ding, SW and Wu, Q},
title = {Culture-Independent Discovery of Viroids by Deep Sequencing and Computational Algorithms.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2316},
number = {},
pages = {251-274},
pmid = {34845701},
issn = {1940-6029},
abstract = {Viroids are single-stranded circular RNA molecules that cause diseases in plants and do not encode any protein. Classical approaches for the identification of new viroids are challenging for many plant pathology laboratories as viroid cDNA synthesis and sequencing require purification and enrichment of the naked viroid RNA by two-dimensional gel electrophoresis. Conventional metagenomic approaches are not effective for viroid discovery because the total number of known viroids is small, and distinct viroids share limited nucleotide sequence similarity. In this chapter, we describe a homology-independent approach for the identification of both known and new viroids in disease samples. It is known that viroid infection of plants triggers production of overlapping viroid-derived small interfering RNAs (siRNAs) targeting the entire genome with high densities and that replication of viroids occurs via a rolling-circle mechanism to yield head-to-tail multiple-repeat replicative intermediates. Our approach involves deep sequencing of either long or small RNAs in a disease sample followed by viroid identification with a unique computational algorithm, progressive filtering of overlapping small RNAs (PFOR). Among the sequenced total small RNAs, PFOR retains viroid-derived siRNAs for viroid genome assembly by progressively eliminating nonoverlapping small RNAs and those that overlap but cannot be assembled into a direct repeat RNA, a unique feature of viroid RNA replication. In contrast, long RNAs sequenced after depletion of ribosomal RNAs are cut into 21-nucleotide virtual overlapping small RNAs with the algorithm SLS (splitting longer read into shorter fragments) before PFOR. We show that new viroids or viroids from the two known families are readily identified and their full-length sequences recovered by PFOR from long or small RNAs sequenced directly from infected plants. We propose that our approach can be used for viroid discovery in both plants and potentially animals since PFOR identifies viroids by searching for circular RNAs or a unique replication intermediate of the viroid genome in a sequence homology-independent manner.},
}

@article {pmid34845444,
year = {2021},
author = {Mzava, O and Cheng, AP and Chang, A and Smalling, S and Kounatse, LD and Lenz, J and Longman, R and Steadman, A and Salvatore, M and Suthanthiran, M and Lee, JR and Mason, CE and Dadhania, D and De Vlaminck, I},
title = {A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2021.11.22.469599},
pmid = {34845444},
abstract = {Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass. Here, we present contamination-free metagenomic DNA sequencing (Coffee-seq), a metagenomic sequencing assay that is robust against environmental contamination. The core idea of Coffee-seq is to tag the DNA in the sample prior to DNA isolation and library preparation with a label that can be recorded by DNA sequencing. Any contaminating DNA that is introduced in the sample after tagging can then be bioinformatically identified and removed. We applied Coffee-seq to screen for infections from microorganisms with low burden in blood and urine, to identify COVID-19 co-infection, to characterize the urinary microbiome, and to identify microbial DNA signatures of inflammatory bowel disease in blood.},
}

@article {pmid34845152,
year = {2021},
author = {Niles, DT and Revell, PA and Ruderfer, D and Marquez, L and McNeil, JC and Palazzi, DL},
title = {Clinical Impact of Plasma Metagenomic Next-generation Sequencing in a Large Pediatric Cohort.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000003395},
pmid = {34845152},
issn = {1532-0987},
abstract = {BACKGROUND: Plasma metagenomic next-generation sequencing (mNGS) has the potential to detect thousands of different organisms with a single test. There are limited data on the real-world impact of mNGS and even less guidance on the types of patients and clinical scenarios in which mNGS testing is beneficial.

METHODS: A retrospective review of patients who had mNGS testing as part of routine clinical care at Texas Children's Hospital from June 2018-August 2019 was performed. Medical records were reviewed for pertinent data. An expert panel of infectious disease physicians adjudicated each unique organism identified by mNGS for clinical impact.

RESULTS: There were 169 patients with at least one mNGS test. mNGS identified a definitive, probable or possible infection in 49.7% of patients. mNGS led to no clinical impact in 139 patients (82.2%), a positive impact in 21 patients (12.4%), and a negative impact in 9 patients (5.3%). mNGS identified a plausible cause for infection more often in immunocompromised patients than in immunocompetent patients (55.8% vs. 30.0%, P = 0.006). Positive clinical impact was highest in patients with multiple indications for testing (37.5%, P = 0.006) with deep-seated infections, overall, being most often associated with a positive impact.

CONCLUSION: mNGS testing has a limited real-world clinical impact when ordered indiscriminately. Immunocompromised patients with well-defined deep-seated infections are likely to benefit most from testing. Further studies are needed to evaluate the full spectrum of clinical scenarios for which mNGS testing is impactful.},
}

@article {pmid34845024,
year = {2021},
author = {Rybarski, JR and Hu, K and Hill, AM and Wilke, CO and Finkelstein, IJ},
title = {Metagenomic discovery of CRISPR-associated transposons.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {49},
pages = {},
doi = {10.1073/pnas.2112279118},
pmid = {34845024},
issn = {1091-6490},
abstract = {CRISPR-associated Tn7 transposons (CASTs) co-opt cas genes for RNA-guided transposition. CASTs are exceedingly rare in genomic databases; recent surveys have reported Tn7-like transposons that co-opt Type I-F, I-B, and V-K CRISPR effectors. Here, we expand the diversity of reported CAST systems via a bioinformatic search of metagenomic databases. We discover architectures for all known CASTs, including arrangements of the Cascade effectors, target homing modalities, and minimal V-K systems. We also describe families of CASTs that have co-opted the Type I-C and Type IV CRISPR-Cas systems. Our search for non-Tn7 CASTs identifies putative candidates that include a nuclease dead Cas12. These systems shed light on how CRISPR systems have coevolved with transposases and expand the programmable gene-editing toolkit.},
}

@article {pmid34844317,
year = {2022},
author = {Chen, S and Holyoak, M and Liu, H and Bao, H and Ma, Y and Dou, H and Jiang, G},
title = {Effects of spatially heterogeneous warming on gut microbiota, nutrition and gene flow of a heat-sensitive ungulate population.},
journal = {The Science of the total environment},
volume = {806},
number = {Pt 1},
pages = {150537},
doi = {10.1016/j.scitotenv.2021.150537},
pmid = {34844317},
issn = {1879-1026},
abstract = {Effects of climate warming on trophic cascades are increasingly reported for large herbivores occupying northern latitudes. During the last 40 years, moose (Alces alces) in northeast China have lost nearly half of their historical distribution through their habitat shifting northwards. There are many possible causes of bottom-up and top-down effects of temperature and for moose in northeast China they are poorly understood. Of particular relevance are the effects of extrinsic environmental factors on gene flow, nutritional adaptions, and gut microbiota that occur as moose populations retreat northwards. We combined molecular biology, nutritional ecology and metagenomics to gain deeper mechanistic insights into the effects of temperature on moose populations. In this study, we revealed that the direction and intensity of gene flow is consistent with global warming driving retreats of moose populations. We interpret this as evidence for the northward movement of moose populations, with cooler northern populations receiving more immigrants and warmer southern populations supplying emigrants. Comparison across latitudes showed that warmer late spring temperatures were associated with plant community composition and facilitated related changes in moose protein and carbohydrate intake through altering forage availability, forage quality and diet composition. Furthermore, these nutrient shifts were accompanied by changes in gut microbial composition and functional pathways related to nutrient metabolism. This study provided insights into mechanisms driving effects of spatial heterogeneous warming on genetic, nutritional and physiological adaptions related to key demographic rates and patterns of survival of heat-sensitive ungulates along a latitude gradient. Understanding such changes helps to identify key habitat areas and plant species to ensure accurate assessment of population status and targeted management of moose populations.},
}

@article {pmid34844054,
year = {2021},
author = {Padhy, SR and Bhattacharyya, P and Dash, PK and Nayak, SK and Parida, SP and Baig, MJ and Mohapatra, T},
title = {Elucidation of dominant energy metabolic pathways of methane, sulphur and nitrogen in respect to mangrove-degradation for climate change mitigation.},
journal = {Journal of environmental management},
volume = {303},
number = {},
pages = {114151},
doi = {10.1016/j.jenvman.2021.114151},
pmid = {34844054},
issn = {1095-8630},
abstract = {Mangroves play a key role in ecosystem balancing and climate change mitigation. It acts as a source and sink of methane (CH4), a major greenhouse gas responsible for climate change. Energy metabolic pathways of methane production (methanogenesis) and oxidation (methanotrophy) are directly driven by sulphur (S) and nitrogen (N) metabolism and salinity in coastal wetlands. To investigate, how mangrove-degradations, affect the source-sink behaviour of CH4; the pathways of CH4, S and N were studied through whole-genome metagenomic approach. Soil samples were collected from degraded and undisturbed mangrove systems in Sundarban, India. Structural and functional microbial diversities (KEGG pathways) of CH4, S and N metabolism were analysed and correlated with labile carbon pools and physico-chemical properties of soil. Overall, the acetoclastic pathway of methanogenesis was dominant. However, the relative proportion of conversion of CO2 to CH4 was more in degraded mangroves. Methane oxidation was higher in undisturbed mangroves and the serine pathway was dominant. After serine, the ribulose monophosphate pathway of CH4 oxidation was dominant in degraded mangrove, while the xylulose monophosphate pathway was dominant in undisturbed site as it is more tolerant to salinity and higher pH. The assimilatory pathway (AMP) of S-metabolism was dominant in both systems. But in AMP pathway, adenosine triphosphate sulfurylase enzyme reads were higher in degraded mangrove, while NADPH-sulfite reductase abundance was higher in undisturbed mangrove due to higher salinity, and pH. In N-metabolism, the denitrification pathway was predominant in degraded sites, whereas the dissimilatory nitrate reduction pathway was dominant in undisturbed mangroves. The relative ratios of sulphur reducing bacteria (SRB): methanogens were higher in degraded mangrove; however, methanotrophs:methanogens was higher in undisturbed mangrove indicated lower source and greater sink capacity of CH4 in the system. Microbial manipulation in mangrove-rhizosphere for regulating major energy metabolic pathways of methane could open-up a new window of climate change mitigation in coastal wetlands.},
}

@article {pmid34843867,
year = {2021},
author = {Novak, B and Lopes Hasuda, A and Ghanbari, M and Mayumi Maruo, V and Bracarense, APFRL and Neves, M and Emsenhuber, C and Wein, S and Oswald, IP and Pinton, P and Schatzmayr, D},
title = {Effects of Fusarium metabolites beauvericin and enniatins alone or in mixture with deoxynivalenol on weaning piglets.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {112719},
doi = {10.1016/j.fct.2021.112719},
pmid = {34843867},
issn = {1873-6351},
abstract = {The impact of the Fusarium-derived metabolites beauvericin, enniatin B and B1 (EB) alone or in combination with deoxynivalenol (DON) was investigated in 28-29 days old weaning piglets over a time period of 14 days. The co-application of EB and DON (EB + DON) led to a significant decrease in the weight gain of the animals. Liver enzyme activities in plasma were significantly decreased at day 14 in piglets receiving the EB + DON-containing diet compared to piglets receiving the control diet. All mycotoxin-contaminated diets led to moderate to severe histological lesions in the jejunum, the liver and lymph nodes. Shotgun metagenomics revealed a significant effect of EB-application on the gut microbiota. Our results provide novel insights into the harmful impact of emerging mycotoxins alone or with DON on the performance, gut health and immunological parameters in pigs.},
}

@article {pmid34843827,
year = {2021},
author = {Di Gaspero, G and Radovic, S and De Luca, E and Spadotto, A and Magris, G and Falginella, L and Cattonaro, F and Marroni, F},
title = {Evaluation of sensitivity and specificity in RNA-Seq-based detection of grapevine viral pathogens.},
journal = {Journal of virological methods},
volume = {},
number = {},
pages = {114383},
doi = {10.1016/j.jviromet.2021.114383},
pmid = {34843827},
issn = {1879-0984},
abstract = {Virus detection is a crucial step for the implementation of clean stock programs that preserve healthy crop species. Viral infections in grapevine, a vegetatively propagated perennial crop, cannot be eradicated from the vineyards by the application of agrochemicals and must be curtailed at the stage of nursery production during the propagation of planting material. Viral detection is routinely performed using enzyme-linked immunosorbent assays (ELISA) or Reverse Transcription-quantitative Polymerase Chain Reactions (RT-qPCR). High throughput sequencing (HTS) approaches have the potential to detect all viral pathogens in a plant specimen. However, to date, no published HTS-based study has used threshold selection based on ROC curves for discriminating positive from negative samples. To fill this gap, we assessed the specificity and sensitivity of different sequencing and bioinformatics approaches for nine common viruses, which were tested in the same specimens using ELISA and/or RT-qPCR. The normalized detection thresholds giving the best results were 19.28 Fragments Per Kilobase of transcript per Million mapped reads (FPKM) for alignment-based total RNA-Seq approaches, 386 Reads Per Million mapped reads (RPM) for metagenomics-based total RNA-Seq, 1,572 FPKM for alignment-based small RNA-Seq analysis and 0.97% of contigs for de novo analysis of small RNA-Seq data. Validation of the proposed thresholds using independent specimens collected over time from the same stocks and other specimens collected from nearby stocks that had derived from the same propagating material showed that HTS approaches are accurate, with RNA-Seq approaches showing better performance than small RNA-Seq.},
}

@article {pmid34842379,
year = {2021},
author = {Victoria Rombot, D and Yermia Semuel, M},
title = {The Metagenomic Analysis of Potential Pathogenic Emerging Bacteria in Fleas.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {24},
number = {10},
pages = {1084-1090},
doi = {10.3923/pjbs.2021.1084.1090},
pmid = {34842379},
issn = {1812-5735},
abstract = {Background and Objective: At present many pathogenic microbes that cause disease in humans are transmitted through animals. Ctenocephalides felisis specific ectoparasites in cats. Metagenomic research on the digestive tract and body surface of C. felishas been conducted. DNA genomics was extracted from the body surface and digestive tract of C. felis. Materials and Methods: Metagenomic analysis has used the 16S rRNA gene (V3-V4 region). Sequencing was carried out using New Generation Sequencing at the First BASE Laboratory, Singapore. Results: Wolbachia has the most significant bacterial composition in C. felis (94.4%), we were found bacteria with a composition >1% that have never been reported to be associated with C. felis. Also, there were 0.2% of bacteria whose taxonomic status cannot be determined. Conclusion: The results of this study become a vital reference pathogenic bacteria that can be transmitted to humans and animals through C. felis. It is necessary to study the resistance of bacteria isolated fromC. felisto antibiotics in the future.},
}

@article {pmid34841779,
year = {2021},
author = {Yin, Y and Yu, R and Chen, H},
title = {[Shotgun metagenome sequencing of Chinese gut microbiota: a review].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {37},
number = {11},
pages = {3717-3733},
doi = {10.13345/j.cjb.210556},
pmid = {34841779},
issn = {1872-2075},
mesh = {China ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; United States ; },
abstract = {The research on the relationship between gut microbiota and human health continues to be a hot topic in the field of life science. Culture independent 16S rRNA gene high-throughput sequencing is the current main research method. However, with the reduction of sequencing cost and the maturity of data analysis methods, shotgun metagenome sequencing is gradually becoming an important method for the study of gut microbiome due to its advantages of obtaining more information. With the support from the human microbiome project, 30 805 metagenome samples were sequenced in the United States. By searching NCBI PubMed and SRA databases, it was found that 72 studies collecting about 10 000 Chinese intestinal samples were used for metagenome sequencing. To date, only 56 studies were published, including 16 related to metabolic diseases, 16 related to infectious and immune diseases, and 12 related to cardiovascular and cerebrovascular diseases. The samples were mainly collected in Beijing, Guangzhou, Shanghai and other cosmopolitan cities, where great differences exist in sequencing platforms and methods. The outcome of most studies are based on correlation analysis, which has little practical value in guiding the diagnosis and treatment of clinical diseases. Standardizing sampling methods, sequencing platform and data analysis process, and carrying out multi center parallel research will contribute to data integration and comparative analysis. Moreover, insights into the functional verification and molecular mechanism by using the combination of transcriptomics, proteomics and culturomics will enable the gut microbiota research to better serve the clinical diagnosis and treatment.},
}

China
*Gastrointestinal Microbiome/genetics
Humans
Metagenome
*Microbiota
RNA, Ribosomal, 16S/genetics
United States

@article {pmid34841352,
year = {2021},
author = {Gómez-Godínez, LJ and Martínez-Romero, E and Banuelos, J and Arteaga-Garibay, RI},
title = {Tools and challenges to exploit microbial communities in agriculture.},
journal = {Current research in microbial sciences},
volume = {2},
number = {},
pages = {100062},
pmid = {34841352},
issn = {2666-5174},
abstract = {Plants contain diverse microbial communities. The associated microorganisms confer advantages to the host plant, which include growth promotion, nutrient absorption, stress tolerance, and pathogen and disease resistance. In this review, we explore how agriculture is implementing the use of microbial inoculants (single species or consortia) to improve crop yields, and discuss current strategies to study plant-associated microorganisms and how their diversity varies under unconventional agriculture. It is predicted that microbial inoculation will continue to be used in agriculture.},
}

@article {pmid34841316,
year = {2021},
author = {Kumar, A and Dubey, A and Malla, MA and Dames, J},
title = {Pyrosequencing and phenotypic microarray to decipher bacterial community variation in Sorghum bicolor (L.) Moench rhizosphere.},
journal = {Current research in microbial sciences},
volume = {2},
number = {},
pages = {100025},
pmid = {34841316},
issn = {2666-5174},
abstract = {Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities as well as soil health. This study investigated, for the first time, keystone microbial taxa inhabiting the rhizosphere of sweet sorghum (Sorghum bicolor) under extensive cultivation practices at three different field sites of South Africa (North West-South (ASHSOIL1); Mpumalanga-West - (ASHSOIL2); and Free State-North West - (ASHSOIL3)). Soil analysis of these sites revealed differences in P, K, Mg, and pH. 16S rRNA amplicon sequencing data revealed that the rhizosphere bacterial microbiome differed significantly both in the structure and composition across the samples. The sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8%, and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Putative metabolic requirements analyzed by METAGENassist software revealed the ASHSOIL1 sample as the prominent ammonia degrader (21.1%), followed by ASHSOIL3 (17.3%) and ASHSOIL2 (11.1%). The majority of core-microbiome taxa were found to be from Cyanobacteria, Bacteroidetes, and Proteobacteria. Functionally, community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. This study showed that soil pH and nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in the sorghum rhizosphere across the different sites.},
}

@article {pmid34840367,
year = {2021},
author = {Ma, R and Cai, TT and Li, H},
title = {Optimal Permutation Recovery in Permuted Monotone Matrix Model.},
journal = {Journal of the American Statistical Association},
volume = {116},
number = {535},
pages = {1358-1372},
pmid = {34840367},
issn = {0162-1459},
support = {R01 GM123056/GM/NIGMS NIH HHS/United States ; R01 GM129781/GM/NIGMS NIH HHS/United States ; },
abstract = {Motivated by recent research on quantifying bacterial growth dynamics based on genome assemblies, we consider a permuted monotone matrix model Y = ΘΠ+ Z, where the rows represent different samples, the columns represent contigs in genome assemblies and the elements represent log-read counts after preprocessing steps and Guanine-Cytosine (GC) adjustment. In this model, Θ is an unknown mean matrix with monotone entries for each row, Π is a permutation matrix that permutes the columns of Θ, and Z is a noise matrix. This paper studies the problem of estimation/recovery of Π given the observed noisy matrix Y. We propose an estimator based on the best linear projection, which is shown to be minimax rate-optimal for both exact recovery, as measured by the 0-1 loss, and partial recovery, as quantified by the normalized Kendall's tau distance. Simulation studies demonstrate the superior empirical performance of the proposed estimator over alternative methods. We demonstrate the methods using a synthetic metagenomics dataset of 45 closely related bacterial species and a real metagenomic dataset to compare the bacterial growth dynamics between the responders and the non-responders of the IBD patients after 8 weeks of treatment.},
}

@article {pmid34839011,
year = {2021},
author = {Becker, A and Pierre Schmartz, G and Gröger, L and Grammes, N and Galata, V and Philippeit, H and Weiland, J and Ludwig, N and Meese, E and Tierling, S and Walter, J and Schwiertz, A and Spiegel, J and Wagenpfeil, G and Faßbender, K and Keller, A and Unger, MM},
title = {Effects of Resistant Starch on Symptoms, Fecal Markers and Gut Microbiota in Parkinson's Disease - the RESISTA-PD Trial.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.gpb.2021.08.009},
pmid = {34839011},
issn = {2210-3244},
abstract = {The composition of the gut microbiome is linked to multiple diseases, including Parkinson's disease (PD). Bacteria producing short-chain fatty acids (SCFAs) and fecal SCFA concentrations are reduced in PD. SCFAs exert various beneficial functions in humans. In the interventional, monocentric, open-label clinical trial "The Effects of Resistant Starch on Bowel Habits, Short Chain Fatty Acids and Gut Microbiota in Parkinson Disease" (RESISTA-PD, NCT02784145), we aimed at altering fecal SCFAs by an 8-week prebiotic intervention with resistant starch (RS). We enrolled 87 subjects in three study-arms: 32 PD patients received RS (PD + RS), 30 control subjects received RS, and 25 PD patients received solely dietary instructions. We performed paired-end 100 base-pair length metagenomic sequencing of fecal samples using the BGISEQ platform at an average of 9.9 GB. RS was well-tolerated. In PD + RS, fecal butyrate concentrations increased significantly, and fecal calprotectin concentrations dropped significantly after 8 weeks of RS. Clinically, we observed a reduction in non-motor symptoms load in PD + RS. The reference-based analysis of metagenomes highlighted stable alpha-diversity and beta-diversity across the three groups, including bacteria producing SCFAs. Reference-free analysis suggested punctual, yet pronounced differences in the metagenomic signature in PD + RS. RESISTA-PD highlights that a prebiotic treatment with RS is safe and well-tolerated in PD. The stable alpha-diversity and beta-diversity alongside altered fecal butyrate and calprotectin concentrations call for long-term studies, also investigating whether RS is able to modify the clinical course of PD.},
}

@article {pmid34838907,
year = {2021},
author = {Zhang, T and Li, J and Wang, N and Wang, H and Yu, L},
title = {Metagenomic analysis reveals microbiome and resistome in the seawater and sediments of Kongsfjorden (Svalbard, High Arctic).},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {151937},
doi = {10.1016/j.scitotenv.2021.151937},
pmid = {34838907},
issn = {1879-1026},
abstract = {Kongsfjorden in the high Arctic, a typical Arctic fjord, experienced long-time input of nutrients and pollutants from the remote and local resources, providing a platform for characterizing the diversity and distribution of antibiotic resistance genes (ARGs). However, the microbiome and antibiotic resistome in this pristine marine system have not been well documented. The present study aimed to identify the diversity and distribution of bacterial communities and associated ARGs in seawater (12 samples) and sediments (13 samples) of Kongsfjorden via metagenomic analysis. In terms of both bacterial community compositions and ARGs profiles, the seawater was significantly distinct from sediment. Only 29 ARG subtypes were detected in the Arctic seawater and sediments. Furthermore, three geochemical factors (i.e., longitude, depth, and PO43-) greatly influenced the bacterial communities in sediment samples, while longitude, depth, and latitude were crucial geochemical factors influencing the ARGs profiles in sediment samples. Procrustes analysis revealed a significant correlation between bacterial community compositions and ARG profiles in seawater and sediment samples. Network analysis further revealed the co-occurrence of metagenome-assembled genomes (MAGs) with ARG subtypes. Overall, our study provides insights into the microbiome and resistome in a pristine Arctic fjord, thereby providing vital information for environmental management.},
}

@article {pmid34837955,
year = {2021},
author = {Yan, Y and Yi, X and Duan, Y and Jiang, B and Huang, T and Inglis, BM and Zheng, B and Si, W},
title = {Alteration of the gut microbiota in rhesus monkey with spontaneous osteoarthritis.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {328},
pmid = {34837955},
issn = {1471-2180},
abstract = {BACKGROUND: The spontaneous osteoarthritis (OA) in rhesus macaque is similar to OA in human, which maintains an upright body posture and shows very similar biomechanical properties of bones to humans. At present, there is no good treatment for OA. This study aims to explore relationship between OA and intestinal microbiota, and provide a reference for the treatment of clinical OA.

RESULTS: We collected colonic contents of the 20 rhesus macaque (6-15 years old, female) for intestinal microbiota analysis by metagenomics sequencing, of which 10 were spontaneous OA monkeys and 10 were normal monkeys. Our results showed the diversity of gut microbiota in monkeys with OA was decreased compared to the normal monkeys (p = 0.16). Mollicutes, Tenericutes, Coprobacillus and Faecalitalea may be biomarkers for the monkeys of OA. Lactobacillus found significantly increased in OA monkeys. Prevotella and Ruminococcus were higher in the normal group than OA group. Zinc/manganese transport system permease protein (p = 0.0011) and Cyclopropane-fatty-acyl-phospholipid synthase (p = 0.0012) are a microbiota metabolic pathway related to cartilage production.

CONCLUSIONS: Our results indicate that the diversity and composition of intestinal microbiota in monkeys with OA are different compared to the normal monkeys. we have found microbes that may be a biomarker for the diagnosis of osteoarthritis. Functional analysis of the microbiota also predicts cartilage damage in the monkeys with osteoarthritis. Non-human primates are closely related to humans, so this study can provide a reference for the development of drugs for the treatment of OA.},
}

@article {pmid34838558,
year = {2021},
author = {Zhu, L and Yuan, H and Shi, Z and Deng, L and Yu, Z and Li, Y and He, Q},
title = {Metagenomic insights into the effects of various biocarriers on moving bed biofilm reactors for municipal wastewater treatment.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {151904},
doi = {10.1016/j.scitotenv.2021.151904},
pmid = {34838558},
issn = {1879-1026},
abstract = {Preferable biocarrier is vital for start-up and operation of moving bed biofilm reactor (MBBR). Effects of three separate biocarriers - PPC, PU, and PP on MBBRs were systematically investigated including nutrients removal performances, biomass attachment, microbial community, and relevant functional genes. Results showed that three biocarriers achieved similar removal efficiencies for chemical oxygen demand (COD) and total phosphorus (TP), though much higher biomasses were found attached onto PPC and PU carriers. PPC and PU performed better than PP for ammonia nitrogen (NH4+-N) removal. However, PPC exhibited the greatest and most reliable denitrifying efficiency, mainly due to stronger simultaneous nitrification and denitrification during better micro-anoxic-environment created within PPC carriers than others. Further studies by 16S rRNA gene and metagenomic sequencing analysis uncovered the bacterial diversity and structures, and relevant functional genes for nitrogen-transformation and pathways of nitrogen metabolisms, which laid the biological basis for the best performances via biocarrier PPC. This study inspired a feasible approach for municipal wastewater treatment through PPC filled MBBR.},
}

@article {pmid34838398,
year = {2021},
author = {Yang, P and Zhong, G and Yang, J and Zhao, L and Sun, D and Tian, Y and Li, R and Rong, L},
title = {Metagenomic and metabolomic profiling reveals the correlation between the microbiota and flavor compounds and nutrients in fermented sausages.},
journal = {Food chemistry},
volume = {},
number = {},
pages = {131645},
doi = {10.1016/j.foodchem.2021.131645},
pmid = {34838398},
issn = {1873-7072},
abstract = {Understanding the interrelationships between the differentially abundant microorganisms and metabolites of traditional "Fuet" fermented sausages (FSs) and inoculated fermented sausages (IFSs) can help us identify key species that are missing from commercial starter cultures to reproduce the flavor compounds and nutrients of traditional Fuet FSs. IFSs, inoculated with P. pentosaceus, P. acidilactici, S. xylosus, S. carnosus (SBM-52) or P. pentosaceus, and S. xylosus (THM-17), were deficient in reproducing the volatilome profile (in particular esters, methyl aldehydes, and methyl ketones) of traditional Fuet FSs because of the lack of diverse Staphylococci (S. carnosus, S. xylosus, S. equorum, and S. saprophyticus). Moreover, the combination of Pediococcus and Staphylococcus were positively associated with amino acid, fatty acid, l-anserine, and l-carnosine levels. Pyridoxal and indolelactic acid levels were significantly increased in IFSs with the addition of P. acidilactici and S. carnosus, which were positively associated with vitamin B6 and tryptophan metabolic pathways.},
}

@article {pmid34838016,
year = {2021},
author = {He, J and He, X and Ma, Y and Yang, L and Fang, H and Shang, S and Xia, H and Lian, G and Tang, H and Wang, Q and Wang, J and Lin, Z and Wen, J and Liu, Y and Zhai, C and Wang, W and Jiang, X and Xuan, J and Liu, M and Lu, S and Li, X and Wang, H and Ouyang, C and Cao, M and Lin, A and Zhang, B and Wu, D and Chen, Y and Xiao, C},
title = {A comprehensive approach to stool donor screening for faecal microbiota transplantation in China.},
journal = {Microbial cell factories},
volume = {20},
number = {1},
pages = {216},
pmid = {34838016},
issn = {1475-2859},
support = {81730003//national natural science foundation of china/ ; 82004433//national natural science foundation of china/ ; 2017ZX09304021//national major science and technology projects of china/ ; 16CZX064//national office for philosophy and social sciences/ ; },
abstract = {BACKGROUND: Faecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridium difficile infections and chronic gastrointestional infections. However, the risks of FMT and the selection process of suitable donors remain insufficiently characterized. The eligibility rate for screening, underlying microbial basis, and core ethical issues of stool donors for FMT are yet to be elucidated in China.

RESULTS: The potential stool donors were screened from December 2017 to December 2019 with the help of an online survey, clinical assessments, and stool and blood testing. Bioinformatics analyses were performed, and the composition and stability of gut microbiota in stool obtained from eligible donors were dynamically observed using metagenomics. Meanwhile, we build a donor microbial evaluation index (DoMEI) for stool donor screening. In the screening process, we also focused on ethical principles and requirements. Of the 2071 participants, 66 donors were selected via the screening process (3.19% success rate). Although there were significant differences in gut microbiota among donors, we found that the changes in the gut microbiota of the same donor were typically more stable than those between donors over time.

CONCLUSIONS: DoMEI provides a potential reference index for regular stool donor re-evaluation. In this retrospective study, we summarised the donor recruitment and screening procedure ensuring the safety and tolerability for FMT in China. Based on the latest advances in this field, we carried out rigorous recommendation and method which can assist stool bank and clinicians to screen eligible stool donor for FMT.},
}

@article {pmid34837814,
year = {2021},
author = {Raza, S and Shin, H and Hur, HG and Unno, T},
title = {Higher abundance of core antimicrobial resistant genes in effluent from wastewater treatment plants.},
journal = {Water research},
volume = {208},
number = {},
pages = {117882},
doi = {10.1016/j.watres.2021.117882},
pmid = {34837814},
issn = {1879-2448},
abstract = {Wastewater treatment plants (WWTPs) receive sewage water from a variety of sources, including livestock farms, hospitals, industries, and households, that contain antimicrobial resistant bacteria (ARB) and antimicrobial resistant genes (ARGs). Current treatment technologies are unable to completely remove ARB and ARGs, which are eventually released into the aquatic environment. This study focused on the core resistome of urban WWTPs that are persistent through wastewater treatment processes. We adopted the Hiseq-based metagenomic sequencing approach to identify the core resistome, their genetic context, and pathogenic potential of core ARGs in the influent (IN) and effluent (EF) samples of 12 urban WWTPs in South Korea. In this study, the abundance of ARGs ranged from 0.32 to 3.5 copies of ARGs per copy of the 16S rRNA gene, where the IN samples were relatively higher than the EF samples, especially for the macrolide-lincosamide-streptogramin (MLS)- and tetracycline- resistant genes. On the other hand, there were 43 core ARGs sharing up to 90% of the total, among which the relative abundance of sul1, APH(3'')-lb, and RbpA was higher in EF than in IN (p < 0.05). Moreover, tetracycline and sulfonamide-related core ARGs in both EF and IN were significantly more abundant on plasmids than on chromosomes (p < 0.05). We also found that the majority of core ARGs were carried by opportunistic pathogens such as Acinetobacter baumannii, Enterobacter cloacae, and Pseudomonas aeruginosa in both IN and EF. In addition, phages were the only mobile elements whose abundance correlated with that of core ARGs in EF, suggesting that transduction may play a major role in disseminating ARGs in the receiving water environment of the urban WWTP. The persistent release of core ARGs with pathogenic potential into environmental water is of immediate concern. The mobility of ARGs and ARBs in the environment is a major public health concern. These results should be taken into consideration when developing policy to mitigate environmental dissemination of ARG by WWTPs.},
}

@article {pmid34837111,
year = {2021},
author = {Roumagnac, P and Lett, JM and Fiallo-Olivé, E and Navas-Castillo, J and Zerbini, FM and Martin, DP and Varsani, A},
title = {Establishment of five new genera in the family Geminiviridae: Citlodavirus, Maldovirus, Mulcrilevirus, Opunvirus, and Topilevirus.},
journal = {Archives of virology},
volume = {},
number = {},
pages = {},
pmid = {34837111},
issn = {1432-8798},
abstract = {Geminiviruses are plant-infecting, circular single-stranded DNA viruses that have a geminate virion morphology. These viruses infect both cultivated and non-cultivated monocotyledonous and dicotyledonous plants and have a wide geographical distribution. Nine genera had been established within the family Geminiviridae (Becurtovirus, Begomovirus, Capulavirus, Curtovirus, Eragrovirus, Grablovirus, Mastrevirus, Topocuvirus, and Turncurtovirus) as of 2020. In the last decade, metagenomics approaches have facilitated the discovery and identification of many novel viruses, among them numerous highly divergent geminiviruses. Here, we report the establishment of five new genera in the family Geminiviridae (Citlodavirus, Maldovirus, Mulcrilevirus, Opunvirus, and Topilevirus) to formally classify twelve new, divergent geminiviruses.},
}

@article {pmid34836555,
year = {2021},
author = {Hwang, Y and Schulze-Makuch, D and Arens, FL and Saenz, JS and Adam, PS and Sager, C and Bornemann, TLV and Zhao, W and Zhang, Y and Airo, A and Schloter, M and Probst, AJ},
title = {Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {234},
pmid = {34836555},
issn = {2049-2618},
support = {39231/ERC_/European Research Council/International ; Nachwuchsgruppe Dr. Alexander Probst//ministerium für innovation, wissenschaft und forschung des landes nordrhein-westfalen/ ; 1553211//national science foundation/ ; DISPERS (50WB1922)//Deutsches Zentrum für Luft- und Raumfahrt/ ; },
abstract = {BACKGROUND: The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core.

RESULTS: Genome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins.

CONCLUSION: We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca. Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems. Video Abstract.},
}

@article {pmid34836550,
year = {2021},
author = {Ter Horst, AM and Santos-Medellín, C and Sorensen, JW and Zinke, LA and Wilson, RM and Johnston, ER and Trubl, GG and Pett-Ridge, J and Blazewicz, SJ and Hanson, PJ and Chanton, JP and Schadt, CW and Kostka, JE and Emerson, JB},
title = {Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {233},
pmid = {34836550},
issn = {2049-2618},
support = {start-up//university of california, davis/ ; DE-SC0021198//u.s. department of energy/ ; DE-SC0020163//u.s. department of energy/ ; DE-SC0007144//u.s. department of energy/ ; DE-SC0012088//u.s. department of energy/ ; SCW1478//u.s. department of energy/ ; Microbiome SFA SCW1632//u.s. department of energy/ ; LLNL LDRD 18-ERD-041//u.s. department of energy/ ; GI Community Sequencing Award #2017//u.s. department of energy/ ; DE-AC05-1008 00OR22725//office of science/ ; },
abstract = {BACKGROUND: Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems.

RESULTS: Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes.

CONCLUSIONS: Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics. Video abstract The importance of Minnesota peat viromes in revealing terrestrial and aquatic niche partitioning for viral populations.},
}

@article {pmid34836316,
year = {2021},
author = {Enaud, R and Cambos, S and Viaud, E and Guichoux, E and Chancerel, E and Marighetto, A and Etchamendy, N and Clark, S and Mohammedi, K and Cota, D and Delhaes, L and Gatta-Cherifi, B},
title = {Gut Microbiota and Mycobiota Evolution Is Linked to Memory Improvement after Bariatric Surgery in Obese Patients: A Pilot Study.},
journal = {Nutrients},
volume = {13},
number = {11},
pages = {},
pmid = {34836316},
issn = {2072-6643},
abstract = {Patients with obesity are known to exhibit gut microbiota dysbiosis and memory deficits. Bariatric surgery (BS) is currently the most efficient anti-obesity treatment and may improve both gut dysbiosis and cognition. However, no study has investigated association between changes of gut microbiota and cognitive function after BS. We prospectively evaluated 13 obese patients on anthropometric data, memory functions, and gut microbiota-mycobiota before and six months after BS. The Rey Auditory Verbal Learning Test (AVLT) and the symbol span (SS) of the Weschler Memory Scale were used to assess verbal and working memory, respectively. Fecal microbiota and mycobiota were longitudinally analyzed by 16S and ITS2 rRNA sequencing respectively. AVLT and SS scores were significantly improved after BS (AVLT scores: 9.7 ± 1.7 vs. 11.2 ± 1.9, p = 0.02, and SS scores: 9.7 ± 23.0 vs. 11.6 ± 2.9, p = 0.05). An increase in bacterial alpha-diversity, and Ruminococcaceae, Prevotella, Agaricus, Rhodotorula, Dipodascus, Malassezia, and Mucor were significantly associated with AVLT score improvement after BS, while an increase in Prevotella and a decrease in Clostridium, Akkermansia,&nbsp;Dipodascus and Candida were linked to SS scores improvement. We identified several changes in the microbial communities that differ according to the improvement of either the verbal or working memories, suggesting a complex gut-brain-axis that evolves after BS.},
}

@article {pmid34836246,
year = {2021},
author = {Lutsiv, T and Weir, TL and McGinley, JN and Neil, ES and Wei, Y and Thompson, HJ},
title = {Compositional Changes of the High-Fat Diet-Induced Gut Microbiota upon Consumption of Common Pulses.},
journal = {Nutrients},
volume = {13},
number = {11},
pages = {},
pmid = {34836246},
issn = {2072-6643},
support = {3060-21650-001-08S//Agricultural Research Service/ ; },
abstract = {The gut microbiome is involved in the host's metabolism, development, and immunity, which translates to measurable impacts on disease risk and overall health. Emerging evidence supports pulses, i.e., grain legumes, as underutilized nutrient-dense, culinarily versatile, and sustainable staple foods that promote health benefits through modulating the gut microbiota. Herein, the effects of pulse consumption on microbial composition in the cecal content of mice were assessed. Male mice were fed an obesogenic diet formulation with or without 35% of the protein component comprised by each of four commonly consumed pulses-lentil (Lens culinaris L.), chickpea (Cicer arietinum L.), common bean (Phaseolus vulgaris L.), or dry pea (Pisum sativum L.). Mice consuming pulses had distinct microbial communities from animals on the pulse-free diet, as evidenced by β-diversity ordinations. At the phylum level, animals consuming pulses showed an increase in Bacteroidetes and decreases in Proteobacteria and Firmicutes. Furthermore, α-diversity was significantly higher in pulse-fed animals. An ecosystem of the common bacteria that were enhanced, suppressed, or unaffected by most of the pulses was identified. These compositional changes are accompanied by shifts in predicted metagenome functions and are concurrent with previously reported anti-obesogenic physiologic outcomes, suggestive of microbiota-associated benefits of pulse consumption.},
}