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Bibliography on: Metagenomics

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ESP: PubMed Auto Bibliography 27 May 2022 at 01:31 Created: 

Metagenomics

While genomics is the study of DNA extracted from individuals — individual cells, tissues, or organisms — metagenomics is a more recent refinement that analyzes samples of pooled DNA taken from the environment, not from an individual. Like genomics, metagenomic methods have great potential in many areas of biology, but none so much as in providing access to the hitherto invisible world of unculturable microbes, often estimated to comprise 90% or more of bacterial species and, in some ecosystems, the bulk of the biomass. A recent describes how this new science of metagenomics is beginning to reveal the secrets of our microbial world: The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation. Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members.

Created with PubMed® Query: metagenomic OR metagenomics OR metagenome NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

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RevDate: 2022-05-26

Sharma R, Kumar R, Sharma A, et al (2022)

Long-term consumption of green tea EGCG enhances murine healthspan by mitigating multiple aspects of cellular senescence in mitotic and post-mitotic tissues, gut dysbiosis, and immunosenescence.

The Journal of nutritional biochemistry pii:S0955-2863(22)00139-5 [Epub ahead of print].

Cellular senescence is emerging as a major hallmark of aging, and its modulation presents an effective anti-aging strategy. This study attempted to understand the progression of cellular senescence in vivo, and whether it can be mitigated by chronic consumption of green tea catechin epigallocatechin gallate (EGCG). We profiled cellular senescence in various organs of mice at four different time-points of lifespan, and then explored the influence of EGCG consumption in impacting markers of cellular senescence, inflamm-aging, immunosenescence, and gut dysbiosis. We report that visceral adipose and intestinal tissues are highly vulnerable to cellular senescence due to an increase in DNA damage response, activation of cell cycle inhibitors, and SASP regulators. With advancing age, dysregulation in nutrient signaling mediators (AMPK/AKT/SIRT3/5), and a decrease in autophagy was also observed. Inflamm-aging markers (TNF-α/IL-1β) and splenic CD4/CD8 T cell ratio increased with age, while NK cell population decreased. Metagenomic analyses revealed an age-related decrease in the diversity of microbial species and an increase in the abundance of various pathogenic bacterial species. On the other hand, long-term EGCG consumption significantly attenuated markers of DNA damage, cell cycle inhibitors, SASP regulators, AMPK/AKT signaling, and enhanced SIRT3/5 expression and autophagy. Systemic inflamm-aging indicators decreased, while early T cell activation increased in EGCG fed animals. EGCG also suppressed the abundance of pathogenic bacteria and preserved microbial diversity. Our results suggest that adipose and intestine tissues are prone to cellular senescence and that chronic consumption of EGCG can attenuate several deleterious aspects of aging which could be implicated in developing anti-aging strategies.

RevDate: 2022-05-26

Huang G, Qu Q, Wang M, et al (2022)

Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates.

The Science of the total environment pii:S0048-9697(22)03275-2 [Epub ahead of print].

Multiple factors influence gut microbiome diversity in vertebrate hosts. Most previous studies have only investigated specific factors and certain host species or taxa. However, a comprehensive assessment of the relative contributions of individual factors towards gut microbial diversity within a broader evolutionary context remains lacking. Here, 2202 16S rRNA gene sequencing samples of gut bacterial communities collected from 452 host species across seven classes were analyzed together to understand the factors broadly affecting vertebrate gut microbiomes across hosts with different diets, threatened status, captivity status, and habitat environmental factors. Among wild vertebrates, diet was most significantly associated with gut microbiome alpha diversity, while host phylogeny and diet were significantly associated with beta diversity, consistent with a previous study. Host threatened status and habitat environmental factors (e.g., geography and climate) were also associated with gut bacterial community beta diversity. Subsequent ecological modeling revealed a strong association between stochastic assembly processes and patterns of gut bacterial diversity among free-ranging vertebrates. In addition, metagenomic analysis of gut microbiomes from 62 captive vertebrates and sympatric humans revealed similar diversity and resistome profiles despite differences in host phylogeny, diet, and threatened status. These results thus suggest that captivity diminishes the effects of host phylogeny, diet, and threatened status on the diversity of vertebrate gut bacterial communities. The most overrepresented antibiotic resistant genes (ARGs) observed in these samples are involved in resistance to β-lactams, aminoglycosides, and tetracycline. These results also revealed potential horizontal transfers of ARGs between captive animals and humans, thereby jointly threatening public health and vertebrate conservation. Together, this study provides a comprehensive overview of the diversity and resistomes of vertebrate gut microbiomes. These combined analyses will help guide future vertebrate conservation via the rational manipulation of microbial diversity and reducing antibiotic usage.

RevDate: 2022-05-26

Zhang Z, Zhou H, Cao H, et al (2022)

Human-to-human transmission of Chlamydia psittaci in China, 2020: an epidemiological and aetiological investigation.

The Lancet. Microbe pii:S2666-5247(22)00064-7 [Epub ahead of print].

BACKGROUND: Chlamydia psittaci can infect a wide range of avian species, occasionally causing psittacosis (also known as parrot fever) in humans. Most human psittacosis cases are associated with close contact with pet birds or poultry. In December, 2020, an outbreak of severe community-acquired pneumonia of unknown aetiology was reported in a hospital in Shandong province, China, and some of the patients' close contacts had respiratory symptoms. Our aims were to determine the causative agent of this epidemic and whether there had been human-to-human transmission.

METHODS: For this epidemiological and aetiological investigation study, we enrolled patients who had community-acquired pneumonia confirmed by chest CT at two local hospitals in Shandong Province in China. We collected sputum, bronchoalveolar lavage fluid, and nasopharyngeal swab samples from participants and detected pathogens by surveying for 22 target respiratory microbes using a commercial assay, followed by metagenomic next-generation sequencing, specific nested PCR, and qPCR tests. We excluded individuals who were C psittaci-negative on both tests. We recruited close contacts of the C psittaci-positive patients, and tested nasopharyngeal swabs from the close contacts and samples from ducks from the processing plant where these patients worked. We then integrated the epidemiological, clinical, and laboratory data to reveal the potential chain of transmission of C psittaci that characterised this outbreak.

FINDINGS: Between Dec 4 and 29, 2020, we used metagenomic next-generation sequencing and different PCR-based approaches to test 12 inpatients with community-acquired pneumonia, of whom six (50%) were workers at a duck-meat processing plant and two (17%) were unemployed people, who were positive for C psittaci and enrolled in this study. We contacted 61 close contacts of the six patients who worked at the duck-meat processing plant, of whom 61 (100%) were enrolled and tested, and we determined that the community-acquired pneumonia outbreak was caused by C psittaci. Within the outbreak cluster, 17 (77%) of 22 participants had confirmed C psittaci infections and five (23%) of 22 participants were asymptomatic C psittaci carriers. The outbreak had begun with avian-to-human transmission, and was followed by secondary and tertiary human-to-human transmission, which included transmission by several asymptomatic carriers and by health-care workers. In addition, some of the participants with confirmed C psittaci infection had no identified source of infection, which suggested cryptic bacterial transmission.

INTERPRETATION: Our study data might represent the first documented report of human-to-human transmission of C psittaci in China. Therefore, C psittaci has the potential to evolve human-to-human transmission via various routes, should be considered an elevated biosecurity and emergent risk, and be included as part of the routine diagnosis globally, especially for high-risk populations.

FUNDING: Academic Promotion Programme of Shandong First Medical University, National Science and Technology Major Project, ARC Australian Laureate Fellowship.

RevDate: 2022-05-26

Liu C, Li G, Qin X, et al (2022)

Profiles of antibiotic- and heavy metal-related resistance genes in animal manure revealed using a metagenomic analysis.

Ecotoxicology and environmental safety, 239:113655 pii:S0147-6513(22)00495-X [Epub ahead of print].

Farmed animals produce excrement containing excessive amounts of toxic heavy metals as a result of consuming compound feed as well as receiving medical treatments, and the presence of these heavy metals may aggravate the risk of spreading drug-resistance genes through co-selection during manure treatment and application processes. However, research on the association between heavy metals and antimicrobial resistance is still lacking. In this study, metagenomic sequencing was used to explore the effects of the co-selection of environmentally toxic heavy metals on the resistome in manure. A relevance network analysis showed that metal-resistance genes (MRGs), especially for copper (Cu) and zinc (Zn), were positively correlated with multiple types of antibiotic-resistance genes (ARGs) and formed a complex network. Most bacteria that co-occurred with both MRGs and ARGs simultaneously are members of Proteobacteria and accounted for 54.7% of the total microbial species in the relevance network. The remaining bacteria belonged to Firmicutes, Bacteroidetes and Actinobacteria. Among the four phyla, Cu- and Zn-resistance genes had more complex correlations with ARGs than other MRG types, reflecting the occurrence of ARG co-selection under the selective pressure of high Cu and Zn levels. In addition, approximately 64.8%, 59.1% and 68.4% of MRGs that correlated with the presence of plasmids, viruses and prophages, respectively, are Cu- or Zn-resistant, and they co-occurred with various ARGs, indicating that mobile genetic elements participate in mediating ARG co-selection in response to Cu and Zn pressure. The results indicated that the use of heavy-metal additives in feed induces the increases of drug resistance genes in manure through co-selection, aggravating the risk of antimicrobial resistance diffusion from animal farm to manure land applications.

RevDate: 2022-05-26

Bae SS, Dong TS, Wang J, et al (2022)

Altered Gut Microbiome in Patients With Dermatomyositis.

ACR open rheumatology [Epub ahead of print].

OBJECTIVE: The study objective was to compare the microbial composition of patients with dermatomyositis (DM) and healthy controls (HCs) and determine whether microbial alterations are associated with clinical manifestations of DM.

METHODS: The 16S ribosomal RNA gene sequencing was performed on fecal samples from patients with DM and HCs. Microbial composition and diversity were compared between subjects with DM and HCs and in association with several DM-specific clinical variables, including myositis-specific autoantibodies (MSAs). Differentially abundant microbial taxa and genes associated with clinical characteristics were identified, and functional analysis was performed using predicted metagenomics. Dietary intake was assessed using a 24-hour dietary recall.

RESULTS: The fecal microbiome of 36 patients with DM and 26 HCs were analyzed. Patients with DM trended toward lower microbial diversity compared with HCs. The higher physician global damage score was significantly correlated with the lower microbial diversity in patients with DM. Patients with interstitial lung disease (ILD)-associated MSA (antisynthetase antibody (ab), anti-melanoma differentiation-associated protein 5 ab, n = 12) had significant differences in microbial composition and lower microbial diversity compared with HCs. Differential abundance testing demonstrated a unique taxonomic signature in the ILD-MSA subgroup, and predictive metagenomics identified functional alterations in a number of metabolic pathways. A significant increase in the relative abundance of Proteobacteria was positively correlated with multiple pathways involved in lipopolysaccharide synthesis and transport in the ILD-MSA group.

CONCLUSION: Patients with DM, particularly with ILD-associated MSAs, have lower microbial diversity and a distinct taxonomic composition compared with HCs. Further studies are needed to validate our findings and elucidate specific pathogenetic mechanisms that link the gut microbiome to clinical and pathological features of DM.

RevDate: 2022-05-26

Cao D, Pang M, Wu D, et al (2022)

Alterations in the Gut Microbiota of Tibetan Patients With Echinococcosis.

Frontiers in microbiology, 13:860909.

There are two main types of echinococcosis, namely alveolar echinococcosis (AE) and cystic echinococcosis (CE). They are zoonotic parasitic diseases caused by the metacestodes of Echinococcus multilocularis and Echinococcus granulosus. In order to explore the gut microbiome composition of patients with echinococcosis, we analyzed fecal samples of seven patients with AE, six patients with CE, and 13 healthy individuals from the Qinghai-Tibetan Plateau, China. Using metagenomic next-generation sequencing, we identified fecal bacteria in the patients with AE and CE. The gut microbiota was analyzed by next-generation metagenomic sequencing (mNGS) to compare patients with either AE or CE against healthy individuals. We found there were some differences between them in abundant bacteria. Our results led to five findings: (1) Between patients with echinococcosis and healthy individuals, the differential bacteria were from four phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria. (2) Rothia mucilaginosa, Veillonella dispar, Veillonella atypica, Streptococcus parasanguinis, Streptococcus salivarius, and Alistipes finegoldii were abundant in the feces of patients with AE. (3) Bacteroides dorei, Parabacteroides distasonis, Escherichia sp_E4742, and Methanobrevibacter smithii were abundant in the feces of the patients with CE. (4) At the phylum and class level, compared to the AE group, the healthy group was characterized by higher numbers of Actinobacteria. (5) At the family level, Lachnospiraceae and Eubacteriaceae were more abundant in the feces of healthy individuals than in AE patients. The genera Coprococcus, Eubacterium, and Bilophia were more abundant in the healthy group, while the genus Rothia was more abundant in the AE group. The results of this study enrich our understanding of the gut microbiome composition of patients with AE and CE in the Qinghai-Tibetan Plateau.

RevDate: 2022-05-25

Zhang Y, Bhosle A, Bae S, et al (2022)

Discovery of bioactive microbial gene products in inflammatory bowel disease.

Nature [Epub ahead of print].

Microbial communities and their associated bioactive compounds1-3 are often disrupted in conditions such as the inflammatory bowel diseases (IBD)4. However, even in well-characterized environments (for example, the human gastrointestinal tract), more than one-third of microbial proteins are uncharacterized and often expected to be bioactive5-7. Here we systematically identified more than 340,000 protein families as potentially bioactive with respect to gut inflammation during IBD, about half of which have not to our knowledge been functionally characterized previously on the basis of homology or experiment. To validate prioritized microbial proteins, we used a combination of metagenomics, metatranscriptomics and metaproteomics to provide evidence of bioactivity for a subset of proteins that are involved in host and microbial cell-cell communication in the microbiome; for example, proteins associated with adherence or invasion processes, and extracellular von Willebrand-like factors. Predictions from high-throughput data were validated using targeted experiments that revealed the differential immunogenicity of prioritized Enterobacteriaceae pilins and the contribution of homologues of von Willebrand factors to the formation of Bacteroides biofilms in a manner dependent on mucin levels. This methodology, which we term MetaWIBELE (workflow to identify novel bioactive elements in the microbiome), is generalizable to other environmental communities and human phenotypes. The prioritized results provide thousands of candidate microbial proteins that are likely to interact with the host immune system in IBD, thus expanding our understanding of potentially bioactive gene products in chronic disease states and offering a rational compendium of possible therapeutic compounds and targets.

RevDate: 2022-05-25

Iwańska O, Latoch P, Suchora M, et al (2022)

Lake microbiome and trophy fluctuations of the ancient hemp rettery.

Scientific reports, 12(1):8846.

Lake sediments not only store the long-term ecological information including pollen and microfossils but are also a source of sedimentary DNA (sedDNA). Here, by the combination of traditional multi-proxy paleolimnological methods with the whole-metagenome shotgun-sequencing of sedDNA we were able to paint a comprehensive picture of the fluctuations in trophy and bacterial diversity and metabolism of a small temperate lake in response to hemp retting, across the past 2000 years. Hemp retting (HR), a key step in hemp fibre production, was historically carried out in freshwater reservoirs and had a negative impact on the lake ecosystems. In Lake Slone, we identified two HR events, during the late stage of the Roman and Early Medieval periods and correlated these to the increased trophy and imbalanced lake microbiome. The metagenomic analyses showed a higher abundance of Chloroflexi, Planctomycetes and Bacteroidetes and a functional shift towards anaerobic metabolism, including degradation of complex biopolymers such as pectin and cellulose, during HR episodes. The lake eutrophication during HR was linked to the allochthonous, rather than autochthonous carbon supply-hemp straws. We also showed that the identification of HR based on the palynological analysis of hemp pollen may be inconclusive and we suggest the employment of the fibre count analysis as an additional and independent proxy.

RevDate: 2022-05-25

Luo T, Guo Z, Liu D, et al (2022)

Deficiency of PSRC1 accelerates atherosclerosis by increasing TMAO production via manipulating gut microbiota and flavin monooxygenase 3.

Gut microbes, 14(1):2077602.

Maladaptive inflammatory and immune responses are responsible for intestinal barrier integrity and function dysregulation. Proline/serine-rich coiled-coil protein 1 (PSRC1) critically contributes to the immune system, but direct data on the gut microbiota and the microbial metabolite trimethylamine N-oxide (TMAO) are lacking. Here, we investigated the impact of PSRC1 deletion on TMAO generation and atherosclerosis. We first found that PSRC1 deletion in apoE-/- mice accelerated atherosclerotic plaque formation, and then the gut microbiota and metabolites were detected using metagenomics and untargeted metabolomics. Our results showed that PSRC1 deficiency enriched trimethylamine (TMA)-producing bacteria and functional potential for TMA synthesis and accordingly enhanced plasma betaine and TMAO production. Furthermore, PSRC1 deficiency resulted in a proinflammatory colonic phenotype that was significantly associated with the dysregulated bacteria. Unexpectedly, hepatic RNA-seq indicated upregulated flavin monooxygenase 3 (FMO3) expression following PSRC1 knockout. Mechanistically, PSRC1 overexpression inhibited FMO3 expression in vitro, while an ERα inhibitor rescued the downregulation. Consistently, PSRC1-knockout mice exhibited higher plasma TMAO levels with a choline-supplemented diet, which was gut microbiota dependent, as evidenced by antibiotic treatment. To investigate the role of dysbiosis induced by PSRC1 deletion in atherogenesis, apoE-/- mice were transplanted with the fecal microbiota from either apoE-/- or PSRC1-/-apoE-/- donor mice. Mice that received PSRC1-knockout mouse feces showed an elevation in TMAO levels, as well as plaque lipid deposition and macrophage accumulation, which were accompanied by increased plasma lipid levels and impaired hepatic cholesterol transport. Overall, we identified PSRC1 as an atherosclerosis-protective factor, at least in part, attributable to its regulation of TMAO generation via a multistep pathway. Thus, PSRC1 holds great potential for manipulating the gut microbiome and alleviating atherosclerosis.

RevDate: 2022-05-25

Fong SB, Boyer E, Bonnaure-Mallet M, et al (2022)

Microbiota in Periodontitis: Advances in the Omic Era.

Advances in experimental medicine and biology, 1373:19-43.

The complexity of the oral microbiome continues to astound researchers even with the advancement of multi-disciplinary strategies being used to study these microorganisms in relation to the human body. There is extensive literature available that explains how oral bacterial communities exist within the biofilm and maintains a balance with the host immune system, but when this balance is tipped disease can occur. The purpose of this review is to highlight the subgingival microbial compositions during health and periodontal disease using next generation sequencing techniques, as well as determining the types of functional activities that partake during these states. The subgingival microbiota is a fluid structure that can adapt accordingly to the environment and the identification of signature biomarkers may aid in the assessment of risk and disease severity in an individual to complement clinical diagnosis in the future.

RevDate: 2022-05-25

Lin GS, Zhao MM, Li XQ, et al (2022)

A Case Report of Infective Endocarditis with Failure of the Empirical Treatment-Q Fever Endocarditis Diagnosed by Metagenomic Next-Generation Sequencing.

Infection and drug resistance, 15:2545-2550 pii:361969.

Background: Infective endocarditis (IE) can be caused by a variety of pathogens. Endocarditis due to the Coxiella burnetii (C. burnetii) infection is common in patients with negative blood culture results and usually occurs in patients with previous valvular heart disease, impaired immune function, and during pregnancy. The diagnosis is difficult based on the conventional diagnostic method, and serious adverse outcomes may occur in the case of delayed diagnosis.

Case Report: In the present study, a case of a 43-year-old male patient with previous valvular heart disease was reported. The patient was admitted with a diagnosis of IE, but the etiology was unclear. Accurate diagnosis and treatment were achieved by combining metagenomic next-generation sequencing (mNGS) with Q fever serological antibody assay.

Conclusion: Metagenomic next-generation sequencing has been increasingly applied in clinical practice in recent years to detect the DNA or RNA in samples, and this could play a decisive role in the etiological diagnosis of some infectious diseases.

RevDate: 2022-05-25

Rajput V, Samson R, Yadav R, et al (2022)

Metagenomic mining of Indian river confluence reveal functional microbial community with lignocelluloytic potential.

3 Biotech, 12(6):132.

Microbial carbohydrate-active enzymes (CAZyme) can be harnessed for valorization of Lignocellulosic biomass (LCB) to value-added chemicals/products. The two Indian Rivers Ganges and the Yamuna having different origins and flow, face accumulation of carbon-rich substrates due to the discharge of wastewater from adjoining paper and pulp industries, which could potentially contribute to the natural enrichment of LCB utilizing genes, especially at their confluence. We analyzed CAZyme diversity in metagenomic datasets across the sacred confluence of the Rivers Ganges and Yamuna. Functional annotation using CAZyme database identified a total of 77,815 putative genes with functional domains involved in the catalysis of carbohydrate degradation or synthesis of glycosidic bonds. The metagenomic analysis detected ~ 41% CAZymes catalyzing the hydrolysis of lignocellulosic biomass polymers- cellulose, hemicellulose, lignin, and pectin. The Beta diversity analysis suggested higher CAZyme diversity at downstream region of the river confluence, which could be useful niche for culture-based studies. Taxonomic origin for CAZymes revealed the predominance of bacteria (97%), followed by archaea (1.67%), Eukaryota (0.63%), and viruses (0.7%). Metagenome guided CAZyme diversity of the microflora spanning across the confluence of Ganges-Yamuna River, could be harnessed for biomass and bioenergy applications.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03190-7.

RevDate: 2022-05-24

Sun H, Zhao F, Liu Y, et al (2022)

Probiotics synergized with conventional regimen in managing Parkinson's disease.

NPJ Parkinson's disease, 8(1):62.

Parkinson's disease (PD) is mainly managed by pharmacological therapy (e.g., Benserazide and dopamine agonists). However, prolonged use of these drugs would gradually diminish their dopaminergic effect. Gut dysbiosis was observed in some patients with PD, suggesting close association between the gut microbiome and PD. Probiotics modulate the host's gut microbiota beneficially. A 3-month randomized, double-blind, placebo-controlled clinical trial was conducted to investigate the beneficial effect of probiotic co-administration in patients with PD. Eighty-two PD patients were recruited and randomly divided into probiotic [n = 48; Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8), Benserazide, dopamine agonists] and placebo (n = 34; placebo, Benserazide, dopamine agonists) groups. Finally, 45 and 29 patients from Probio-M8 and placebo groups provided complete fecal and serum samples for further omics analysis, respectively. The results showed that Probio-M8 co-administration conferred added benefits by improving sleep quality, alleviating anxiety, and gastrointestinal symptoms. Metagenomic analysis showed that, after the intervention, there were significantly more species-level genome bins (SGBs) of Bifidobacterium animalis, Ruminococcaceae, and Lachnospira, while less Lactobacillus fermentum and Klebsiella oxytoca in Probio-M8 group (P < 0.05). Interestingly, Lactobacillus fermentum correlated positively with the scores of UPDRS-III, HAMA, HAMD-17, and negatively with MMSE. Klebsiella oxytoca correlated negatively with feces hardness. Moreover, co-administering Probio-M8 increased SGBs involved in tryptophan degradation, gamma-aminobutyric acid, short-chain fatty acids, and secondary bile acid biosynthesis, as well as serum acetic acid and dopamine levels (P < 0.05). Taken together, Probio-M8 synergized with the conventional regimen and strengthened the clinical efficacy in managing PD, accompanied by modifications of the host's gut microbiome, gut microbial metabolic potential, and serum metabolites.

RevDate: 2022-05-24

Otake-Kasamoto Y, Kayama H, Kishikawa T, et al (2022)

Lysophosphatidylserines derived from microbiota in Crohn's disease elicit pathological Th1 response.

The Journal of experimental medicine, 219(7):.

Microbiota alteration and IFN-γ-producing CD4+ T cell overactivation are implicated in Crohn's disease (CD) pathogenesis. However, it remains unclear how dysbiosis enhances Th1 responses, leading to intestinal inflammation. Here, we identified key metabolites derived from dysbiotic microbiota that induce enhanced Th1 responses and exaggerate colitis in mouse models. Patients with CD showed elevated lysophosphatidylserine (LysoPS) concentration in their feces, accompanied by a higher relative abundance of microbiota possessing a gene encoding the phospholipid-hydrolyzing enzyme phospholipase A. LysoPS induced metabolic reprogramming, thereby eliciting aberrant effector responses in both human and mouse IFN-γ-producing CD4+ T cells. Administration of LysoPS into two mouse colitis models promoted large intestinal inflammation. LysoPS-induced aggravation of colitis was impaired in mice lacking P2ry10 and P2ry10b, and their CD4+ T cells were hyporesponsive to LysoPS. Thus, our findings elaborate on the mechanism by which metabolites elevated in patients with CD harboring dysbiotic microbiota promote Th1-mediated intestinal pathology.

RevDate: 2022-05-24

Tong X, Yu X, Du Y, et al (2022)

Peripheral Blood Microbiome Analysis via Noninvasive Prenatal Testing Reveals the Complexity of Circulating Microbial Cell-Free DNA.

Microbiology spectrum [Epub ahead of print].

While circulating cell-free DNA (cfDNA) is becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a microbial cfDNA baseline in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Because noninvasive prenatal testing (NIPT) shares many similarities with the sequencing protocol of metagenomics, we utilized the standard low-pass whole-genome-sequencing-based NIPT to establish a microbial cfDNA baseline in healthy people. Sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening were retrospectively collected and reanalyzed for microbiome DNA screening. It was found that more than 95% of exogenous cfDNA was from bacteria, 3% from eukaryotes, and 0.4% from viruses, indicating the gut/environment origins of many microorganisms. Overall and regional abundance patterns were well illustrated, with huge regional diversity and complexity, and unique interspecies and symbiotic relationships were observed for TORCH organisms (Toxoplasma gondii, others [Treponema pallidum {causing syphilis}, hepatitis B virus {HBV}, and human parvovirus B19 {HPV-B19}], rubella virus, cytomegalovirus [CMV], and herpes simplex virus [HSV]) and another common virus, Epstein-Barr virus (EBV). To sum up, our study revealed the complexity of the baseline circulating microbial cfDNA and showed that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner. IMPORTANCE While circulating cell-free DNA (cfDNA) has been becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a baseline for microbial cfDNA in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Standard low-pass whole-genome-sequencing-based NIPT shares many similarities with the sequencing protocol for metagenomics and could provide a microbial cfDNA baseline in healthy people; thus, a reference cfDNA data set of the human microbiome was established with sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening. Our study revealed the complexity of circulating microbial cfDNA and indicated that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner, especially with regard to geographic patterns and coexistence networks.

RevDate: 2022-05-24
CmpDate: 2022-05-24

Hogle SL, Hackl T, Bundy RM, et al (2022)

Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean.

The ISME journal, 16(6):1636-1646.

Prochlorococcus and Synechococcus are the most abundant photosynthesizing organisms in the oceans. Gene content variation among picocyanobacterial populations in separate ocean basins often mirrors the selective pressures imposed by the region's distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread in Synechococcus and low-light adapted Prochlorococcus populations from deep chlorophyll maximum layers of iron-depleted regions of the oligotrophic Pacific and S. Atlantic oceans: Prochlorococcus siderophore consumers were absent in the N. Atlantic ocean (higher new iron flux) but constituted up to half of all Prochlorococcus genomes from metagenomes in the N. Pacific (lower new iron flux). Picocyanobacterial siderophore consumers, like many other bacteria with this trait, also lack siderophore biosynthesis genes indicating that they scavenge exogenous siderophores from seawater. Statistical modeling suggests that the capacity for siderophore uptake is endemic to remote ocean regions where atmospheric iron fluxes are the smallest, especially at deep chlorophyll maximum and primary nitrite maximum layers. We argue that abundant siderophore consumers at these two common oceanographic features could be a symptom of wider community iron stress, consistent with prior hypotheses. Our results provide a clear example of iron as a selective force driving the evolution of marine picocyanobacteria.

RevDate: 2022-05-23

Zhang J, Fu Q, Huang Y, et al (2022)

Negative impacts of sea-level rise on soil microbial involvement in carbon metabolism.

The Science of the total environment pii:S0048-9697(22)03184-9 [Epub ahead of print].

Sea-level rise has been threatening the terrestrial ecosystem functioning of coastal islands, of which the most important component is carbon (C) cycling. However, metagenomic and metabolomic evidence documenting salt intrusion effects on molecular biological processes of C cycling are still lacking. Here, we investigated microbial communities, metagenomic taxonomy and function, and metabolomic profiles in the marine-terrestrial transition zone of low- and high-tide, and low- and high-land areas based on distances of 0 m, 50 m, 100 m, and 200 m, respectively, to the water-land junction of Neilingding Island. Our results showed that soil salinity (EC) was the dominant driver controlling bacterial abundance and community composition and metagenomic taxonomy and function. The metabolomic profiling at the low-tide site was significantly different from that of other sites. The low-tide site had greater abundance of Proteobacteria and Bacteroidetes (1.6-3.7 fold), especially Gammaproteobacteria, but lower abundance (62-83%) of Acidobacteria and Chloroflexi, compared with other three sites. The metagenomic functional genes related to carbohydrate metabolism decreased at the low-tide site by 15.2%, including the metabolism of aminosugars, di- and oligo-saccharides, glycoside hydrolases, and monosaccharides, leading to significant decreases in 21 soil metabolites, such as monosaccharide (l-gulose), disaccharide (sucrose and turanose), and oligosaccharides (stachyose and maltotetraose). Our study demonstrates that elevated salinity due to sea-level rise may suppress C-cycling genes and their metabolites, therefore having negative impacts on microbial metabolism of organic matter.

RevDate: 2022-05-23

Oliveira Sartori AG, Cesar ASM, Gruchowski Woitowicz FC, et al (2022)

Plant genetic diversity by DNA barcoding to investigate propolis origin.

Phytochemistry pii:S0031-9422(22)00142-X [Epub ahead of print].

Identify the botanical origins of a certain type of propolis may be challenging and time demanding, since it involves bee's behavior observation, plant resins collection and chemical analysis. Thus, this study aimed to determine the plant genetic materials in propolis from southern Brazil using the DNA barcoding to investigate their botanical origins, as well as to compare it with the phytochemical composition determined by ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS) and with the pollinic profile. As principal results, non-native Populus carolinensis Moench (Salicaceae) was almost the only DNA source in some propolis samples, which coincided with the presence of flavonoids typical from poplar exudates. Conversely, other propolis samples had DNA material coming mainly from native plant species, most of them characterized to the species level, although no specific chemical markers from those plants could be identified by UHPLC-HRMS. However, pollen from several plants identified by the DNA barcoding were extracted from some propolis samples. Despite the identification of typical diterpenes, DNA material from Araucaria angustifolia (Bertol.) Kuntze (Araucariaceae), which have been indicated as a major resin source for propolis from preservation areas in southern Brazil, was found in very small abundancies, likely because bees do not drag tissue material containing DNA when collecting resin from this native species. In conclusion, DNA barcoding analysis successfully provided information about the provenance of propolis, although, depending on the plant resin sources, this information is likely to come from pollen.

RevDate: 2022-05-23

Zhou X, Arslan M, Liu Z, et al (2022)

Low carbon-to-nitrogen ratio digestate from high-rate anaerobic baffled reactor facilitates heterotrophic/autotrophic nitrifiers involved in nitrogen removal.

Bioresource technology pii:S0960-8524(22)00675-7 [Epub ahead of print].

In this study, baffled anaerobic-aerobic reactors (AOBRs) with modified basalt fiber (MBF) carriers and felt were used to treat domestic wastewater (DWW). The influent was first treated in anaerobic compartments, with the NH4+-N containing digestate refluxed into aerobic compartment for nitrification. The nitrified liquid was channeled to the anaerobic compartments for further denitrification. Under optimal conditions, AOBR with MBF carriers could remove 91% chemical oxygen demand (COD) and 81% total nitrogen (TN), with biomass production increased by 7.6%, 4.5% and 8.7% in three successive anaerobic compartments compared to the control. Biological viability analysis showed that live cells outnumbered dead cells in bio-nests. Metagenomics analysis showed that multiple metabolic pathways accounted for nitrogen conversion in anaerobic and aerobic compartments. More importantly, low COD/TN ratio digestate facilitated heterotrophic nitrification-aerobic denitrification (HN-AD) species growth in aerobic compartment. This study provides a promising strategy to source treatment of DWW from urban communities.

RevDate: 2022-05-23

Abe Y, Fukushima K, Matsumoto Y, et al (2022)

Mycobacterium senriense sp. nov., a slowly growing, non-scotochromogenic species, isolated from sputum of an elderly man.

International journal of systematic and evolutionary microbiology, 72(5):.

A slowly growing mycobacteria, identified as strain TY59T, was isolated from sputum of an elderly man with pneumonia. Sequencing of the 16S rRNA gene indicated that this strain was similar to members of the Mycobacterium avium complex and closely related species. Strain TY59T has highest 16S rRNA gene sequence similarities to the type strains of Mycobacterium colombiense (99.80 % sequence similarity), Mycobacterium vulneris (99.74 %), Mycobacterium timonense (99.54 %), Mycobacterium avium subsp. avium (99.54 %) and Mycobacterium avium subsp. silvaticum (99.54 %). Analysis of the internal transcribed spacer (ITS) and DNA-directed RNA polymerase subunit beta (rpoB) sequences gave similar results to the 16S rRNA gene analysis. The closest species to strain TY59T were M. colombiense and M. vulneris with 97.90-98.25 % identity in ITS and 96.4-96.6 % in rpoB. The strain's 65 kDa heat shock protein (hsp65) gene was different from those of M. vulneris, M. colombiense and M. avium subsp. silvaticum with 72.4-74.2 % identity. Average nucleotide identity results showed a 93.4 % match to M. vulneris as the maximum value. Phenotypically, the non-chromogenicity, rough colonies, growth at 42 °C, negative results for nitrate reduction, β-glucosidase and Tween 80 hydrolysis, and positive results for catalase activity set this strain apart from closely related species. We propose that Mycobacterium senriense sp. nov. is a novel species of slowly growing mycobacteria. The type strain is TY59T (RIMD 1371001T=CIP 111917T).

RevDate: 2022-05-23

Yu H, Speth DR, Connon SA, et al (2022)

Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep.

Applied and environmental microbiology [Epub ahead of print].

Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b ("Candidatus Methanocomedenaceae") and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. IMPORTANCE Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.

RevDate: 2022-05-23

Zhang Z, Nie S, Sang Y, et al (2022)

Effects of Spartina alterniflora Invasion on Nitrogen Fixation and Phosphorus Solubilization in a Subtropical Marine Mangrove Ecosystem.

Microbiology spectrum [Epub ahead of print].

Nitrogen fixation (NF) and phosphorus solubilization (PS) play a key role in maintaining the stability of mangrove ecosystems. In China, the invasion of Spartina alterniflora has brought a serious threat to the mangrove ecosystem. However, systematic research on NF and PS in mangrove sediments has not been conducted, and limited studies have focused on the response of NF and PS to S. alterniflora invasion, particularly at different sediment depths. In the present study, shotgun metagenomics and quantitative PCR were used to study the 0- to 100-cm sediment profile of the mangrove ecosystem in the Beibu Gulf of China. Results showed that the PS potential of mangrove sediments was primarily caused by enzymes encoded by phoA, phoD, ppx, ppa, and gcd genes. S. alterniflora changed environmental factors, such as total nitrogen, total phosphorus, and total organic carbon, and enhanced the potential of NF and PS in sediments. Moreover, most microorganisms involved in NF or PS (NFOPSMs) responded positively to the invasion of S. alterniflora. Cd, available iron, and salinity were the key environmental factors that affected the distribution of NF and PS genes (NFPSGs) and NFOPSMs. A strong coupling effect was observed between NF and PS in the mangrove ecosystem. S. alterniflora invasion enhanced the coupling of NF and PS and the interaction of microorganisms involved in NF and PS (NFAPSM), thereby promoting the turnover of NP and improving sediment quality. Finally, 108 metagenome-assembled genomes involved in NF or PS were reconstructed to further evaluate NFOPSMs. IMPORTANCE This study revealed the efficient nutrient cycling mechanism of mangroves. Positive coupling effects were observed in sediment quality, NF and PS processes, and NFOPSMs with the invasion of S. alterniflora. This research contributed to the understanding of the effects of S. alterniflora invasion on the subtropical mangrove ecosystem and provided theoretical guidance for mangrove protection, restoration, and soil management. Additionally, novel NFOPSMs provided a reference for the development of marine biological fertilizers.

RevDate: 2022-05-23

Chen T, Xie G, Mi J, et al (2022)

Recovery of the Structure and Function of the Pig Manure Bacterial Community after Enrofloxacin Exposure.

Microbiology spectrum [Epub ahead of print].

At present, growth-promoting antibiotics are banned in the pig industry in many countries, but therapeutic antibiotics can still be used normally. However, the effect of therapeutic antibiotics on the structure and function of the intestinal bacterial community and its recovery is still unclear. We analyzed the effects of enrofloxacin on the pig manure bacterial community and functional genes during dosing and without dosing. Enrofloxacin caused significant changes in community structure. The changes in the diversity and structure of the bacterial community were the most obvious on the fifth day, and most of the differentially abundant genera (19/29) belonged to Firmicutes. The structure of the manure bacterial community in the low concentration enrofloxacin group was completely reverted after 10 days of drug discontinuation. In addition, enrofloxacin had a significant impact on the abundance of bacterial functional genes. Most of the differentially abundant functional genes of the manure bacterial community were significantly enriched, especially genes related to metabolic pathways, for adaptation to the antibiotic environment. Moreover, exposure to enrofloxacin increased the abundance of functional genes related to nitrogen metabolism in the manure bacterial community, and the total nitrogen content of pig manure was significantly reduced. The functional genetic differences caused by enrofloxacin exposure were completely reverted 10 days after drug discontinuation. The results of the present study suggest that enrofloxacin induces changes in the structure and function of manure bacterial communities, which may be rapidly recovered after drug discontinuation. IMPORTANCE A stable intestinal bacterial community balance is beneficial for animal health. Enrofloxacin is widely used in animal husbandry as a therapeutic drug, but it can cause intestinal environmental imbalance. Enrofloxacin is widely present in groundwater, pork, etc., which leads to a greater risk of human exposure. The effect of enrofloxacin on the structure and function of the intestinal bacterial community and its recovery is still unclear. In this study, we found that enrofloxacin, as a therapeutic drug, can enhance nitrogen metabolism in the manure bacterial community. Moreover, the structure and function of the manure bacterial community in the low concentration enrofloxacin group may be completely reverted 10 days after drug discontinuation. This study provides a reference for the effect of enrofloxacin exposure on the intestinal bacterial community.

RevDate: 2022-05-23

Cornet L, Cleenwerck I, Praet J, et al (2022)

Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity.

mSystems [Epub ahead of print].

Snodgrassella is a genus of Betaproteobacteria that lives in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of a few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole-genome sequences of 75 Snodgrassella strains from 4 species of honeybees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early from the other species in their evolution, that isolates from honeybees and bumblebees were well separated, and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees: i.e., Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species- or group-specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes. IMPORTANCE The microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee's microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species (i.e., Snodgrassella alvi), has been named. Here, we demonstrate that this genus is actually composed of at least seven species, two of which (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) are formally described and named in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus.

RevDate: 2022-05-23

Vishnu RA, Alamelu S, Arun KV, et al (2022)

Comparative evaluation of subgingival microbiome in healthy periodontium and gingivitis using next-generation sequencing technology: A case-control study.

Journal of Indian Society of Periodontology, 26(3):224-229.

Background: Human dental plaque is a complex microbial community containing millions of species. Gingivitis is a dysregulated immune-inflammatory response induced by dysbiotic plaque biofilm that interrupts symbiosis. The emergence of next-generation sequencing with 16S rRNA gene has greatly contributed in understanding the complexity of microbiota. However, studies focusing on microbiome in gingivitis are limited. The whole bacterial community is important in causing periodontal disease than a small number of periodontal pathogens. In this study, we attempted to profile the subgingival microbiome from individuals with healthy gingiva and in patients with gingivitis using next-generation sequencing technology.

Materials and Methods: Subgingival plaque samples from 15 healthy periodontium (Group I) and 15 gingivitis (Group II) were collected and 16s rRNA sequencing was done in Illumina Solexa Sequencer. Data analysis using 16s metagenomics tool from BaseSpace onsite operational taxonomic units was assigned to each sequence using HOMD database. Individual variation in the microbiome of the subgingival samples between the two groups was also evaluated.

Results: The comparison of top 20 species between Group I and Group II revealed no significant species group between them. Synergistetes was absent in Group I samples but found in Group II. At the genus level, HACEK group species were found in both the groups, while Dialister and Aneroglobus were found abundantly in the Group II.

Conclusion: The presence of unique genera and species seen in Group II samples could point toward a dysbiotic shift that could be taking place in the subgingival environment leading to gingivitis.

RevDate: 2022-05-23

Ishaq SL, Turner SM, Tudor MS, et al (2022)

Many Questions Remain Unanswered About the Role of Microbial Transmission in Epizootic Shell Disease in American Lobsters (Homarus americanus).

Frontiers in microbiology, 13:824950.

Despite decades of research on lobster species' biology, ecology, and microbiology, there are still unresolved questions about the microbial communities which associate in or on lobsters under healthy or diseased states, microbial acquisition, as well as microbial transmission between lobsters and between lobsters and their environment. There is an untapped opportunity for metagenomics, metatranscriptomics, and metabolomics to be added to the existing wealth of knowledge to more precisely track disease transmission, etiology, and host-microbe dynamics. Moreover, we need to gain this knowledge of wild lobster microbiomes before climate change alters environmental and host-microbial communities more than it likely already has, throwing a socioeconomically critical industry into disarray. As with so many animal species, the effects of climate change often manifest as changes in movement, and in this perspective piece, we consider the movement of the American lobster (Homarus americanus), Atlantic Ocean currents, and the microorganisms associated with either.

RevDate: 2022-05-23

Mahajna A, Dinkla IJT, Euverink GJW, et al (2022)

Clean and Safe Drinking Water Systems via Metagenomics Data and Artificial Intelligence: State-of-the-Art and Future Perspective.

Frontiers in microbiology, 13:832452.

The use of next-generation sequencing technologies in drinking water distribution systems (DWDS) has shed insight into the microbial communities' composition, and interaction in the drinking water microbiome. For the past two decades, various studies have been conducted in which metagenomics data have been collected over extended periods and analyzed spatially and temporally to understand the dynamics of microbial communities in DWDS. In this literature review, we outline the findings which were reported in the literature on what kind of occupancy-abundance patterns are exhibited in the drinking water microbiome, how the drinking water microbiome dynamically evolves spatially and temporally in the distribution networks, how different microbial communities co-exist, and what kind of clusters exist in the drinking water ecosystem. While data analysis in the current literature concerns mainly with confirmatory and exploratory questions pertaining to the use of metagenomics data for the analysis of DWDS microbiome, we present also future perspectives and the potential role of artificial intelligence (AI) and mechanistic models to address the predictive and mechanistic questions. The integration of meta-omics, AI, and mechanistic models transcends metagenomics into functional metagenomics, enabling deterministic understanding and control of DWDS for clean and safe drinking water systems of the future.

RevDate: 2022-05-23

Liu P, Hu S, He Z, et al (2022)

Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome.

Frontiers in microbiology, 13:828254.

Intestinal bacteria strains play crucial roles in maintaining host health. Researchers have increasingly recognized the importance of strain-level analysis in metagenomic studies. Many analysis tools and several cutting-edge sequencing techniques like single cell sequencing have been proposed to decipher strains in metagenomes. However, strain-level complexity is far from being well characterized up to date. As the indicator of strain-level complexity, metagenomic single-nucleotide polymorphisms (SNPs) have been utilized to disentangle conspecific strains. Lots of SNP-based tools have been developed to identify strains in metagenomes. However, the sufficient sequencing depth for SNP and strain-level analysis remains unclear. We conducted ultra-deep sequencing of the human gut microbiome and constructed an unbiased framework to perform reliable SNP analysis. SNP profiles of the human gut metagenome by ultra-deep sequencing were obtained. SNPs identified from conventional and ultra-deep sequencing data were thoroughly compared and the relationship between SNP identification and sequencing depth were investigated. The results show that the commonly used shallow-depth sequencing is incapable to support a systematic metagenomic SNP discovery. In contrast, ultra-deep sequencing could detect more functionally important SNPs, which leads to reliable downstream analyses and novel discoveries. We also constructed a machine learning model to provide guidance for researchers to determine the optimal sequencing depth for their projects (SNPsnp, https://github.com/labomics/SNPsnp). To conclude, the SNP profiles based on ultra-deep sequencing data extend current knowledge on metagenomics and highlights the importance of evaluating sequencing depth before starting SNP analysis. This study provides new ideas and references for future strain-level investigations.

RevDate: 2022-05-23

Jiang M, Yang C, Kwan PSL, et al (2022)

Rapid Multilateral and Integrated Public Health Response to a Cross-City Outbreak of Salmonella Enteritidis Infections Combining Analytical, Molecular, and Genomic Epidemiological Analysis.

Frontiers in microbiology, 13:772489.

On September 21, 2019, the Shenzhen and Dongguan Centers for Disease Control and Prevention received notification of a large cluster of suspected gastroenteritis involving primarily children who sought medical care at hospitals throughout two adjacent cities in China, Shenzhen, and Dongguan. A joint outbreak response was promptly initiated across jurisdictions in a concerted effort between clinical microbiologists, epidemiologists, and public health scientists. Concurrently, multiplex PCRs were used for rapid laboratory diagnosis of suspected cases; epidemiological investigations were conducted to identify the outbreak source, complemented by near real-time multicenter whole-genome analyses completed within 34 h. Epidemiological evidence indicated that all patients had consumed egg sandwiches served on September 20 as snacks to children and staff at a nursery in Dongguan, located near Shenzhen. Salmonella Enteritidis was isolated from case-patients, food handlers, kitchenware, and sandwiches with kitchen-made mayonnaise. Whole-genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis demonstrated a well-supported cluster with pairwise distances of ≤1 SNP between genomes for outbreak-associated isolates, providing the definitive link between all samples. In comparison with historical isolates from the same geographical region, the minimum pairwise distance was >14 SNPs, suggesting a non-local outbreak source. Genomic source tracing revealed the possible transmission dynamics of a S. Enteritidis clone throughout a multi-provincial egg distribution network. The efficiency and scale with which multidisciplinary and integrated approaches were coordinated in this foodborne disease outbreak response was unprecedented in China, leading to the timely intervention of a large cross-jurisdiction Salmonella outbreak.

RevDate: 2022-05-23

Zhao G, Deng X, Wu D, et al (2022)

Application of metagenomic sequencing toward rapid and sensitive diagnosis of goose avastrovirus infection in China.

Veterinary research forum : an international quarterly journal, 13(1):1-6.

The gosling gout, a newly emerged disease, has widely broken out in China since 2017. Typical signs for the disease include diarrhea, anorexia, depression, dehydration, emaciation and paralysis. At autopsy, uratosis was the main pathological change which could be found at kidney, pericardium, air sac, muscle and leg joint. In this study, gosling gout was firstly diagnosed by metagenomic analysis. Samples of kidney, Fabricius bursa, spleen and jejunum were collected and submitted to next-generation DNA sequencing. Our results demonstrated that goose avastrovirus was highly related with this disease. We confirmed the sequencing results by reverse transcription polymerase chain reaction method and artificial infection experiment and got consistent results. In summary, metagenomic sequencing method combined with traditional molecular identification was applied toward diagnosis of a novel gosling gout disease in China and revealed that goose avastrovirus was highly related with this disease. It has been proved to be a powerful tool for rapid and sensitive diagnosis of animal diseases, especially for some exceptional pathogens. In addition, host range, variation, molecular pathogenesis and potential zoonotic infection of this novel goose astrovirus need to be further studied.

RevDate: 2022-05-23

Onohuean H, Agwu E, UU Nwodo (2022)

A Global Perspective of Vibrio Species and Associated Diseases: Three-Decade Meta-Synthesis of Research Advancement.

Environmental health insights, 16:11786302221099406 pii:10.1177_11786302221099406.

Outbreaks of Vibrio infections have a long history of global public health concern and threat to the aquaculture industry. This 3-decade (1990-2019) meta-synthesis of global research progress in Vibrio species and associated disease outbreaks was undertaken to generate the knowledge needed to design effective interventions with policy implications. Using PRISMA protocol, we obtained data on the online version of the Institute for Scientific Information (ISI), Web of Science (WOS), and Scopus from January 1990 to September 2021 by title search of the keywords "Vibrio species OR Vibrio spp. OR vibriosis." On the 3-decade survey, the result has shown that a total of 776 publications document types were published on the subject, with an average of 24.25 ± 13.6 published documents per year with an annual growth rate of 4.71%. The year 2020 recorded the highest output of 52 published documents accounting for 6.70% of the total. The most prolific author, Blanch A., published 12 articles on the subject and has received citations of 1003 with an h-index of 10. While the most global cited paper author is the journal of J. Bacteriol (Bassler et al), receiving total citation (TC) (550) and per Year (22). The top active corresponding authors country is the United States of America with (92) articles, freq. 12.40%; TC of 3103. The observations in this study, such as the collaborations network map, and index, which have outlined a big difference between countries based on economic status, have underscored the need for a sustained research mentorship program that can define future policies.

RevDate: 2022-05-23

Que T, Pang X, Huang H, et al (2022)

Comparative Gut Microbiome in Trachypithecus leucocephalus and Other Primates in Guangxi, China, Based on Metagenome Sequencing.

Frontiers in cellular and infection microbiology, 12:872841.

The Trachypithecus leucocephalus (white-headed langur) is a highly endangered, karst-endemic primate species, inhabiting the karst limestone forest in Guangxi, Southwest China. How white-headed langurs adapted to karst limestone and special dietary remains unclear. It is the first time to study the correlation between the gut microbiome of primates and special dietary, and environment in Guangxi. In the study, 150 fecal samples are collected from nine primates in Guangxi, China. Metagenomic sequencing is used to analyze and compare the gut microbiome composition and diversity between white-headed langurs and other primates. Our results indicate that white-headed langurs has a higher diversity of microbiome than other primates, and the key microbiome are phylum Firmicutes, class Clostridia, family Lachnospiraceae, and genera Clostridiates and Ruminococcus, which are related to the digestion and degradation of cellulose. Ten genera are significantly more abundant in white-headed langurs and François' langur than in other primates, most of which are high-temperature microbiome. Functional analysis reveals that energy synthesis-related pathways and sugar metabolism-related pathways are less abundant in white-headed langurs and François' langur than in other primates. This phenomenon could be an adaptation mechanism of leaf-eating primates to low-energy diet. The gut microbiome of white-headed langurs is related to diet and karst limestone environment. This study could serve as a reference to design conservation breeding, manage conservation units, and determine conservation priorities.

RevDate: 2022-05-23

Zhou J, Fu M, Zhang D, et al (2022)

Metagenomic Next-Generation Sequencing for Accurate Diagnosis of Acute HIV Infection with Aseptic Meningitis: A Case Report.

Infection and drug resistance, 15:2529-2536 pii:361049.

Background: Although individuals infected with HIV for the first time manifest a series of acute syndromes, most patients show mild or no symptoms, which complicates the initial clinical diagnosis. Early diagnosis is important for effective prevention and management of patients. Metagenomic next-generation sequencing technology (mNGS) can rapidly detect a wide range of pathogenic microorganisms, even in atypical cases. However, to date, few studies have reported the application of mNGS to diagnose acute HIV infection with aseptic meningitis.

Case Presentation: A 38-year-old man was admitted to the Department of Infectious Diseases due to repeated fever, headache, and scattered rashes on his limbs. Routine blood analysis revealed elevated absolute lymphocytes and monocytes. Moreover, monocytes were found to be significantly increased following a lumbar puncture and cerebrospinal fluid detection. mNGS results revealed the presence of the human immunodeficiency virus (HIV-1), with HIV RNA of 910 copies/mL in his cerebrospinal fluid. The HIV antigen/antibody test was negative. According to a study by Fie Big et al, a clear diagnosis of acute HIV infection at Fiebig stage I. The patient's condition improved after treatment, and he was prescribed antiretroviral therapy (ART) after discharge.

Conclusion: Aseptic meningitis is easily misdiagnosed during the initial stages of acute HIV infection. mNGS can be used to identify the pathogen early, rapidly, and accurately, thereby improving the treatment of acute HIV infections.

RevDate: 2022-05-23

Hu Q, Li Y, Zhang Y, et al (2022)

Case Report: First Report of T-Cell Large Granular Lymphocytic Leukemia With NPL-DHX9 Gene Fusion Successfully Treated With Cladribine: Clinical Experience and Literature Review.

Frontiers in oncology, 12:824393.

Background: T-cell large granular lymphocytic leukemia (T-LGLL) is a rare lymphoproliferative disorder that starts in T cells and is usually indolent. Long-term use of immunosuppressants, combined with agranulocytosis, is a double-edged sword, as both can lead to serious infections, especially in patients with combined hematologic malignancies and immune defects.

Case Presentation: A 30-year-old female patient was admitted to the hospital because of agranulocytosis for five years, with chest tightness, fatigue, and fever for two days. Pathology and metagenomic next-generation sequencing (mNGS) detected Aspergillus. Although she received cyclosporine and methylprednisolone, the patient showed drug intolerance and progression with invasive pulmonary fungal infections. After a bone marrow aspiration biopsy and other related examinations, she was diagnosed with T-LGLL and invasive pulmonary aspergillosis (IPA). T-cell immunophenotype was CD45+CD3dim+CD5-CD4-CD8+CD7+CD57p+CD25-CD30-, TCRγδ+, transducer and activator of transcripton-3 (STAT3) Y640F mutation and fusion gene NPL-DHX9 rearrangement were confirmed, which has never been reported in hematological diseases. After voriconazole regimen adjustment during treatment based on therapeutic drug concentration monitoring (TDM) and improvement in lung infection, the patient finally treated with purine nucleoside analogues (PNA) cladribine as a single agent at 0.14 mg/kg/d for 5 days. Complete response was achieved after four-cycles cladribine treatment (WBC 2.1*109/L, HGB 117 g/L, PLT 196*109/L, ANC 1.6*109/L, and ALC 0.2*109/L).

Conclusions: To our knowledge, this is the first case of T-LGLL with a rare γδ type and fusion gene NPL-DHX9 rearrangement. The patient was successfully treated with cladribine, suggesting that this regimen could be a promising therapeutic strategy for patients with aggressive T-LGLL.

RevDate: 2022-05-23

Dong N, Jordan AE, Shen X, et al (2022)

Rhino-Orbital Cerebral Mucormycosis in a Patient With Diabetic Ketoacidosis: A Case Report and Literature Review.

Frontiers in neurology, 13:815902.

Background: Rhino-orbital cerebral mucormycosis (ROCM) is a rare, invasive, and fatal fungal disease. Due to the lack of specific clinical manifestations and adequate auxiliary examinations, patients are easily misdiagnosed in the early stage. Early diagnosis and timely therapy are essential for successful treatment.

Case Report: We report a 68-year-old man with diabetic ketoacidosis, presented with orbital apex syndrome (OAS), fever, and pansinusitis, which progressively worsened to death only 4 days after admission. It was finally confirmed as a fungal Rhizopus arrhizus infection by metagenomics cell-free DNA next-generation sequencing (mNGS) testing.

Conclusion: Orbital apex syndrome could be the initial presentation for mucormycosis. Thus, it is necessary to evaluate the presence of mucormycosis in patients with OAS, especially in diabetic or immunosuppressed hosts, and mNGS testing and timely antifungal therapy should be strongly recommended in highly suspected cases.

RevDate: 2022-05-22

Li Y, Guo S, Zheng Y, et al (2022)

Bioimmobilization of lead in phosphate mining wasteland by isolated strain Citrobacter farmeri CFI-01.

Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(22)00699-6 [Epub ahead of print].

Industrial phosphate rock (PR) treatment has introduced lead (Pb) contamination into phosphate mining wasteland, causing serious contamination. Although bioremediation is considered an effective method and studies have investigated the bioimmobilization of Pb contamination in phosphate mining wasteland by phosphate-solubilizing bacteria (PSB), the bioimmobilization mechanism remains unclear. In this study, a strain Citrobacter farmeri CFI-01 with phosphate-solubilizing and Pb-tolerant abilities was isolated from a phosphate mining wasteland. Liquid culture experiments showed that the maximum content of soluble phosphate and the percentage amount of Pb immobilized after 14 days were 351.5 mg/L and 98.18%, respectively, with a decrease in pH. Soil experiments showed that CFI-01 had reasonable bioimmobilization ability, and the percentage amount of Pb immobilized was increased by 7.790% and 22.18% in the groups inoculated with CFI-01, respectively, compared with that of the groups not inoculated with CFI-01. Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), and scanning electron microscopy (SEM) analyses showed that the immobilization of Pb was also ascribed to changes in the functional groups (e.g., hydroxyl and carboxyl groups) and the formation of lead phosphate sediments. Finally, the results of the metagenomic analysis indicated that changes in the microbial community structure, enrichment of related functional abundances (e.g., metal metabolism, carbohydrate metabolism, and amino acid metabolism functions), and activation of functional genes (e.g., zntA, smtB, cadC, ATOX1, smtA, and ATX1) could help immobilize soil Pb contamination and explore the mechanism of bacterial bioimmobilization in Pb-contaminated soil. This study provides insights for exploring the immobilization mechanism of Pb contamination in phosphate mining wasteland using PSB, which has significance for further research.

RevDate: 2022-05-22

Delik A, Dinçer S, Ülger Y, et al (2022)

Metagenomic identification of gut microbiota distribution on the colonic mucosal biopsy samples in patients with non-alcoholic fatty liver disease.

Gene pii:S0378-1119(22)00406-1 [Epub ahead of print].

Backgraund Non-alcoholic fatty liver disease (NAFLD) is known to be the most common liver disease in the world, and there are currently no approved pharmacological treatments to prevent or treat this condition. In addition to being associated with an increased risk of hepatocellular carcinoma and cirrhosis, NAFLD has now become the leading cause of liver failure-associated transplantation. The 16S rRNA gene which conserved regions can serve as universal primer binding sites for PCR amplification of gene fragments, while hypervariable regions contain significant sequence diversity useful for prokaryotic identification purposes. 16S rRNA gene sequences can be use by researchers to identify prokaryotic taxonomy found in clinical samples. As a result of increasing microbiota studies with developing technological developments, the role of intestinal microbiota in the pathogenesis of NAFLD is revealed in an important way. In this study, it was aimed to determine the clinical prognostic importance of gut microbiota in the pathogenesis of NAFLD and to determine the microbial composition with intestinal mucosal biopsy samples in NAFLD patients.

MATERIAL AND METHOD: We included 20 patients diagnosed with NAFLD as a result of liver function tests, histological, ultrasonographic, biopsy evidence and 20 normal control groups created under exclusion criteria in this study. The healthy control group of the same age and gender as the patients were determined to be equal, and the age, gender, BMI, insulin resistance, AST, ALT levels of the individuals were recorded for analysis. İntestinal mucosal biopsy samples were taken from the individuals included in the study under sterile conditions. Microbial results were obtained as a result of 16S rRNA amplicon metagenomic processes. The region of approximately 1500 bp covering the V1-V9 region of the 16S rRNA gene was targeted to detect microbial diversity. The amplified regions were sequenced using next-generation sequencing. Operational Taxonomic Unit (OTU) value was obtained with bioinformatics software with the obtained sequence data. The analysis of the recorded parameters was done with the SPSS.19 statistical program.

RESULTS: In the designed study, 16 phyla, 28 class, 56 order, 128 family, 415 genera, 1041 species microorganisms were analyzed taxonomically in a total of 40 individuals. In our study, Intestinal microbial diversity is lower in NAFLD patients compared to control group individuals. In addition, gram-negative bacteria were found to be more dominant in NAFLD patients. As a phylum, Proteobacteria increased in NAFLD group, Bacteroidetes and Actinobacteria in control group, while Firmicutes had equal distribution in both groups. BMI OR=6.37, 95%CI (0.39-0.40) p value was 0.001 in laboratory data, whereas Proteobacteria OR=1.754, 95% CI (0.901-3.416), p value 0.05 in microbial profile.

CONCLUSION: The 16S rRNA metagenomic study of intestinal microbiota using colonic mucosal biopsy samples in NAFLD disease was the first study in the Turkish population, and important data were obtained for other studies. In the data obtained, we think Proteobacteria, Ruminococcaceae, Escherichia coli and Bacilli are very important in both diagnostic and treatment options as a microbial profile in non-alcoholic fatty liver disease.

RevDate: 2022-05-22

Park C, Kim B, T Park (2022)

DeepHisCoM: deep learning pathway analysis using hierarchical structural component models.

Briefings in bioinformatics pii:6590446 [Epub ahead of print].

Many statistical methods for pathway analysis have been used to identify pathways associated with the disease along with biological factors such as genes and proteins. However, most pathway analysis methods neglect the complex nonlinear relationship between biological factors and pathways. In this study, we propose a Deep-learning pathway analysis using Hierarchical structured CoMponent models (DeepHisCoM) that utilize deep learning to consider a nonlinear complex contribution of biological factors to pathways by constructing a multilayered model which accounts for hierarchical biological structure. Through simulation studies, DeepHisCoM was shown to have a higher power in the nonlinear pathway effect and comparable power for the linear pathway effect when compared to the conventional pathway methods. Application to hepatocellular carcinoma (HCC) omics datasets, including metabolomic, transcriptomic and metagenomic datasets, demonstrated that DeepHisCoM successfully identified three well-known pathways that are highly associated with HCC, such as lysine degradation, valine, leucine and isoleucine biosynthesis and phenylalanine, tyrosine and tryptophan. Application to the coronavirus disease-2019 (COVID-19) single-nucleotide polymorphism (SNP) dataset also showed that DeepHisCoM identified four pathways that are highly associated with the severity of COVID-19, such as mitogen-activated protein kinase (MAPK) signaling pathway, gonadotropin-releasing hormone (GnRH) signaling pathway, hypertrophic cardiomyopathy and dilated cardiomyopathy. Codes are available at https://github.com/chanwoo-park-official/DeepHisCoM.

RevDate: 2022-05-22

Jingushi K, Kawashima A, Saito T, et al (2022)

Circulating extracellular vesicles carrying Firmicutes reflective of the local immune status may predict clinical response to pembrolizumab in urothelial carcinoma patients.

Cancer immunology, immunotherapy : CII [Epub ahead of print].

Bacterial flora has clinical significance for the host. The metabolic environment created by this flora influences immunotherapy in urothelial carcinoma. However, there are no reports on the clinical significance of bacterial flora in the host bloodstream. We aimed to clarify the correlation between extracellular vesicle (EV)-derived blood microflora information and tumor immunological status in urothelial carcinoma (UC) patients. Serum samples were collected from 20 healthy donors, 50 patients with localized UC, and 31 patients with metastatic UC (mUC) who had undergone pembrolizumab treatment. Bacterial DNA in EVs was extracted from each sample. Metagenomic sequencing was performed after amplification of the V1-V2 region of the bacterial 16S rRNA gene. Using the matched tumor tissue and serum samples, we revealed that the smaller amount of peripheral EVs carrying Firmicutes DNA was significantly correlated with the higher number of infiltrating T cells within tumor tissues (CD3; p = 0.015, CD4; p = 0.039, CD8; p = 0.0084) and the higher expression of activation markers on their surface (ICOS on both CD4; p = 0.0013 and CD8 T cells; p = 0.016 and 4-1BB on CD4 T cells; p = 0.016). In terms of circulating metabolic information, L-Ser and L-Pro levels, which play important roles in T cell expansion and proliferation, were significantly higher in the Firmicutes-low group (p = 0.010). All of the patients with higher Firmicutes abundance had disease progression without any clinical response (p = 0.026) and significantly inferior prognosis for pembrolizumab therapy (p = 0.035). This is the first study on the importance of peripheral bacterial EVs in cancer patients treated with cancer immunotherapy.

RevDate: 2022-05-21

Ghuneim LJ, Raghuvanshi R, Neugebauer KA, et al (2022)

Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection.

The ISME journal [Epub ahead of print].

Antibiotics are our primary approach to treating complex infections, yet we have a poor understanding of how these drugs affect microbial communities. To better understand antimicrobial effects on host-associated microbial communities we treated cultured sputum microbiomes from people with cystic fibrosis (pwCF, n = 24) with 11 different antibiotics, supported by theoretical and mathematical modeling-based predictions in a mucus-plugged bronchiole microcosm. Treatment outcomes we identified in vitro that were predicted in silico were: 1) community death, 2) community resistance, 3) pathogen killing, and 4) fermenter killing. However, two outcomes that were not predicted when antibiotics were applied were 5) community profile shifts with little change in total bacterial load (TBL), and 6) increases in TBL. The latter outcome was observed in 17.8% of samples with a TBL increase of greater than 20% and 6.8% of samples with an increase greater than 40%, demonstrating significant increases in community carrying capacity in the presence of an antibiotic. An iteration of the mathematical model showed that TBL increase was due to antibiotic-mediated release of pH-dependent inhibition of pathogens by anaerobe fermentation. These dynamics were verified in vitro when killing of fermenters resulted in a higher community carrying capacity compared to a no antibiotic control. Metagenomic sequencing of sputum samples during antibiotic therapy revealed similar dynamics in clinical samples. This study shows that the complex microbial ecology dictates the outcomes of antibiotic therapy against a polymicrobial infection.

RevDate: 2022-05-21

Kim DW, Jeong HS, Kim E, et al (2022)

Oral delivery of stem-cell-loaded hydrogel microcapsules restores gut inflammation and microbiota.

Journal of controlled release : official journal of the Controlled Release Society pii:S0168-3659(22)00291-7 [Epub ahead of print].

Mesenchymal stem cells (MSCs) are an attractive candidate for the treatment of inflammatory bowel disease (IBD), but their poor delivery rate to an inflamed colon is a major factor hampering the clinical potential of stem cell therapies. Moreover, there remains a formidable hurdle to overcome with regard to survival and homing in to injured sites. Here, we develop a strategy utilizing monodisperse hydrogel microcapsules with a thin intermediate oil layer prepared by a triple-emulsion drop-based microfluidic approach as an in-situ oral delivering carrier. The oral delivery of stem-cell-loaded hydrogel microcapsules (SC-HM) enhances MSC survival and retention in the hostile stomach environment due to the intermediate oil layer and low value of the overall stiffness, facilitating programmable cell release during gastrointestinal peristalsis. SC-HM is shown to induce tissue repair, reduce the colonic macrophage infiltration responsible for the secretion of the pro-inflammatory factors, and significantly mitigate the severity of IBD in a mouse model, where MSCs released by SC-HM successfully accumulate at the colonic crypt. Moreover, a metagenomics analysis reveals that SC-HM ameliorates the dysbiosis of specific bacterial genera, including Bacteroides acidifaciens, Lactobacillus (L.) gasseri, Lactobacillus reuteri, and L. intestinalis, implying optimization of the microorganism's composition and abundance. These findings demonstrate that SC-HM is a potential IBD treatment candidate.

RevDate: 2022-05-21

Che R, Bai M, Xiao W, et al (2022)

Nutrient levels and prokaryotes affect viral communities in plateau lakes.

The Science of the total environment pii:S0048-9697(22)03130-8 [Epub ahead of print].

Viruses are the most abundant organisms in aquatic environments. Recent advances of viral metagenomic have greatly expanded our understanding of aquatic viral communities. However, little is known about the difference of viral communities and driving factors in freshwater lake. This study seeks to understand the spatio-temporal variation, differences, and driving factors of viral communities in two plateau lakes (Dianchi and Fuxian Lakes) with significant nutritional differences. The viral communities exhibited apparent seasonal variation in Dianchi Lake, while seasonal influences on the viral communities were greater than location-based influences. Two-thirds of all detected viral taxa were shared in two lakes, but there was variation in the composition of viral communities. Correlations between prokaryotic communities, environmental factors and viral communities were analyzed. The nutrients, chlorophyll a were primarily environmental parameters affecting viral communities, and the prokaryotic community was significantly correlated with the viral community. In addition, several viruses infecting humans were identified in two lakes, with the most abundant being Herpesviridae and Poxviridae. Overall, these findings provide information on the dynamics, composition, and differences of viral and prokaryotic communities in plateau lakes with different nutrient levels. These results suggest that nutritional levels and prokaryotic communities could play an important role in shaping viral communities in freshwater lakes.

RevDate: 2022-05-21

Liu B, Zhang D, X Pan (2022)

Nodules of wild legumes as unique natural hotspots of antibiotic resistance genes.

The Science of the total environment pii:S0048-9697(22)03133-3 [Epub ahead of print].

Root nodules (RN) of legumes have distinct microenvironment from their symbiotic roots and surrounding soils. The rhizobia can withstand the host-produced phytoalexins and antimicrobial compounds. We thus hypothesize that the wild legume RN may develop unique natural resistome and be antibiotic resistance gene (ARG) hotspots. In this study, in comparison with rhizosphere soil (RS) and bulk soil (BS), we characterized the feature of antibiotic resistance in the RN of two wild legumes, Medicago polymorpha and Astragalus sinicus, by metagenomics. It was shown that the total relative abundance of ARGs followed the order of RN > RS > BS for both legumes. ARGs encoding antibiotic efflux pump predominated in all samples with increased proportion from BS to RN samples for both legumes. Totally 275 ARG subtypes were detected, and diversity of ARGs in RN was significantly lower than in BS samples for both legumes. 32 and 25 unique ARGs subtypes were detected in RN of both legumes. Bacterial community played a key role in shaping nodule-associated resistome because both ARG profiles and bacterial community differed greatly among BS, RS and RN. Rhizobia potentially hosted 10 and 15 ARGs subtypes for both legumes. The number and proportion of plasmid- and ARG-carrying contigs (ACCs) were higher in RN than in BS. Host tracking analysis of plasmid-ACCs suggests that proportion of rhizobial bacteria identified as their hosts decreased from BS to RN samples. No plasmid-ACCs with multiple ARGs were observed in BS samples, whereas they were detected in RN samples of both legumes. Our study showed that even wild legume nodules are unique natural ARG hotspots and enough attention should be paid to the dissemination risk of ARGs posed by globally produced legume crops.

RevDate: 2022-05-21

Ma X, Johnson KB, Gu B, et al (2022)

The in-situ release of algal bloom populations and the role of prokaryotic communities in their establishment and growth.

Water research, 219:118565 pii:S0043-1354(22)00518-8 [Epub ahead of print].

Harmful algal blooms (HABs) may quickly travel and inoculate new water bodies via currents and runoff in estuaries. The role of in-situ prokaryotic communities in the re-establishment and growth of inoculated algal blooms remains unknown. A novel on-board incubation experiment was employed to simulate the sudden surge of algal blooms to new estuarine waters and reveal possible outcomes. A dinoflagellate (Amphidinium carterae) and a diatom species (Thalassiosira weissflogii) which had bloomed in the Pearl River Estuary (PRE) area were cultured to bloom densities and reintroduced back into PRE natural seawaters. The diatom showed better adaptation ability to the new environment and increased significantly after the incubation. Simultaneously, particle-attached (PA) prokaryotic community structure was strongly influenced by adding of the diatom, with some opportunistic prokaryotes significantly enhanced in the diatom treatment. Whereas the dinoflagellate population did not increase following incubation, and their PA prokaryotic community showed no significant differences relative to the control. Metagenomic analyzes revealed that labile carbohydrates and organic nitrogen produced by the diatom contributed to the surge of certain PA prokaryotes. Genomic properties of a bacteria strain, which is affiliated with genus GMD16E07 (Planctomycetaceae) and comprised up to 50% of PA prokaryotes in the diatom treatment, was described here for the first time. Notably, the association of Planctomycetaceae and T. weissflogii likely represents symbiotic mutualism, with the diatom providing organic matter for Planctomycetaceae and the bacteria supplying vitamins and detoxifying nitriles and hydrogen peroxides in exchange. Therefore, the close association between Planctomycetaceae and T. weissflogii promoted the growth of both populations, and eventually facilitated the diatom bloom establishment.

RevDate: 2022-05-21

Wang C, Wang Y, Wang Y, et al (2022)

Impacts of food waste to sludge ratios on microbial dynamics and functional traits in thermophilic digesters.

Water research, 219:118590 pii:S0043-1354(22)00543-7 [Epub ahead of print].

A self-stabilizing microbial community lays the foundation of the efficient biochemical reactions of the anaerobic digestion (AD) process. Despite extensive profiling of microbial community dynamics under varying operating parameters, the effects of food waste (FW) to feeding sewage sludge (FSS) ratios on the microbial assembly, functional traits, and syntrophic interspecies interactions in thermophilic microbial consortia remain poorly understood. Here, we investigated the long-term impacts of the FW: FSS ratio on the thermophilic AD microbiome using genome-centric metagenomics. Both the short reads (SRs) assembly, and the iterative hybrid assembly (IHA) of SRs and nanopore long reads (LRs) were used to reconstruct metagenome-assembled genomes (MAGs) and four microbial clusters were identified, demonstrating different microbial dynamics patterns in response to varying FW:FSS ratios. Cluster C1-C3 were comprised of full functional members with genetic potentials in fulfilling empirical AD biochemical reactions, wherein, syntrophic decarboxylating acetogens could interact with methanogens, and some microbes could be energized by the electron bifurcation mechanism to drive thermodynamics unfavorable reactions. We found the co-existence of both acetogenic and hydrogenotrophic methanogens in the AD microbiome, and they altered their trophic groups to scavenge the methanogenic substrates in ensuring the methane generation in digesters with different FW:FSS ratios. Another interesting observation was that two phylogenetically close Thermotogota species showed a possible strong competition on carbon source inferred by the nearly complete genetic overlap of their relevant pathways.

RevDate: 2022-05-21

Kumar Parida P, Behera BK, Dehury B, et al (2022)

Community structure and function of microbiomes in polluted stretches of river Yamuna in New Delhi, India, using shotgun metagenomics.

Environmental science and pollution research international [Epub ahead of print].

The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization have profoundly affected river microflora and their function thus its health. In this study, potential of whole-genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing) and Syntrophobacter fumaroxidans (sulphate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages was also noticed along the downstream river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e. Nakaseomyces, Aspergillus, Schizosaccharomyces and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase-peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most enriched pollution degrading enzymes in the polluted study sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.

RevDate: 2022-05-20

Tang R, Liu F, Lan Y, et al (2022)

Transcriptomics and metagenomics of common cutworm (Spodoptera litura) and fall armyworm (Spodoptera frugiperda) demonstrate differences in detoxification and development.

BMC genomics, 23(1):388.

BACKGROUND: Spodoptera litura is an important polyphagous pest that causes significant damage to the agricultural sector. We performed RNA-seq of 15 S. litura individuals from larval (fifth and sixth instar larvae), chrysalis, and adult developmental stages. We also compared the S. litura transcriptome data with Spodoptera frugiperda across the same developmental stages, which was sequenced in our previous study.

RESULTS: A total of 101,885 differentially expressed transcripts (DETs) were identified in S. litura. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that S. litura may undergo active xenobiotic and detoxifying metabolism during its larval and adult stages, which may explain difficulties with current population control measures. We also found that DETs of single-copy orthologous genes between S. litura and S. frugiperda were involved in basic metabolism and development. However, energy and metabolic processes genes had a higher expression in S. litura, whereas nervous and olfactory function genes had a higher expression in S. frugiperda. Metagenomics analysis in larval S. litura and S. frugiperda revealed that microbiota participate in the detoxification and metabolism processes, but the relative abundance of detoxification-related microbiota was more abundant in S. frugiperda. Transcriptome results also confirmed the detoxification-related pathway of S. frugiperda was more abundant than in S. litura.

CONCLUSIONS: Significant changes at transcriptional level were identified during the different development stages of S. litura. Importantly, we also identified detoxification associated genes and gut microbiota between S. litura and S. frugiperda at different developmental stages, which will be valuable in revealing possible mechanisms of detoxification and development in these two lepidopterans.

RevDate: 2022-05-20

Shi H, Nelson JW, Phillips S, et al (2022)

Alterations of the gut microbial community structure and function with aging in the spontaneously hypertensive stroke prone rat.

Scientific reports, 12(1):8534.

Gut dysbiosis, a pathological imbalance of bacteria, has been shown to contribute to the development of hypertension (HT), systemic- and neuro-inflammation, and blood-brain barrier (BBB) disruption in spontaneously hypertensive stroke prone rats (SHRSP). However, to date individual species that contribute to HT in the SHRSP model have not been identified. One potential reason, is that nearly all studies of the SHRSP gut microbiota have analyzed samples from rats with established HT. The goal of this study was to examine the SHRSP gut microbiota before, during, and after the onset of hypertension, and in normotensive WKY control rats over the same age range. We hypothesized that we could identify key microbes involved in the development of HT by comparing WKY and SHRSP microbiota during the pre-hypertensive state and longitudinally. Systolic blood pressure (SBP) was measured by tail-cuff plethysmography and fecal microbiota analyzed by16S rRNA gene sequencing. SHRSP showed significant elevations in SBP, as compared to WKY, beginning at 8 weeks of age (p < 0.05 at each time point). Bacterial community structure was significantly different between WKY and SHRSP as early as 4 weeks of age, and remained different throughout the study (p = 0.001-0.01). At the phylum level we observed significantly reduced Firmicutes and Deferribacterota, and elevated Bacteroidota, Verrucomicrobiota, and Proteobacteria, in pre-hypertensive SHRSP, as compared to WKY. At the genus level we identified 18 bacteria whose relative abundance was significantly different in SHRSP versus WKY at the pre-hypertensive ages of 4 or 6 weeks. In an attempt to further refine bacterial candidates that might contribute to the SHRSP phenotype, we compared the functional capacity of WKY versus SHRSP microbial communities. We identified significant differences in amino acid metabolism. Using untargeted metabolomics we found significant reductions in metabolites of the tryptophan-kynurenine pathway and increased indole metabolites in SHRSP versus WKY plasma. Overall, we provide further evidence that gut dysbiosis contributes to hypertension in the SHRSP model, and suggest for the first time the potential involvement of tryptophan metabolizing microbes.

RevDate: 2022-05-20

Gao S, Khan MI, Kalsoom F, et al (2022)

Role of gene regulation and inter species interaction as a key factor in gut microbiota adaptation.

Archives of microbiology, 204(6):342.

Gut microbiota is a class of microbial flora present in various eukaryotic multicellular complex animals such as human beings. Their community's growth and survival are greatly influenced by various factors such as host-pathogen, pathogen-environment and genetic regulation. Modern technologies like metagenomics have particularly extended our capacity to uncover the microbial treasures in challenging conditions like communities surviving at high altitude. Molecular characterizations by newly developed sequencing tools have shown that this complex interaction greatly influences microbial adaptation to the environment. Literature shows that gut microbiota alters the genetic expression and switches to an alternative pathway under the influence of unfavorable conditions. The remarkable adaptability of microbial genetic regulatory networks enables them to survive and expand in tough and energy-limited conditions. Variable prevalence of species in various regions has strengthened this initial evidence. In view of the interconnection of the world in the form of a global village, this phenomenon must be explored more clearly. In this regard, recently there has been significant addition of knowledge to the field of microbial adaptation. This review summarizes and shed some light on mechanisms of microbial adaptation via gene regulation and species interaction in gut microbiota.

RevDate: 2022-05-20

Quaranta G, Mandrioli J, Bibbò S, et al (2022)

Rummeliibacillus suwonensis: First Time Isolation from Human Feces by Culturomics.

Current microbiology, 79(7):197.

Gut microbiota is a complex ecosystem composed by trillions of microorganisms that are crucial for human health or disease status. Currently, there are two methodological options to explore its complexity: metagenomics and culturomics. Culturomics is an approach that uses multiple culture conditions (days of incubation, enrichment factors and growth temperature) and MALDI-TOF mass spectrometry for the identification of bacterial species and sequencing when this method fails. In this paper, we describe how Colturomic's protocol has allowed the first isolation in human sample of Rummeliibacillus suwonensis, a Gram positive, facultative anaerobe bacterium. The bacterium was isolated from feces of a 69 years old male with amyotrophic lateral sclerosis (ALS) recruited for a clinical trial assessing safety and efficacy of fecal microbiota transplantation in ALS. The first isolation of the microorganism dates back to 2013 from the soil of a South Korean mountain area. In this report, morphological description, biochemical characterization and antibiotic susceptibility tests were performed to outline the bacterial properties.

RevDate: 2022-05-20

Price JT, Vwalika B, France M, et al (2022)

HIV-associated vaginal microbiome and inflammation predict spontaneous preterm birth in Zambia.

Scientific reports, 12(1):8573.

A Lactobacillus-deficient, anaerobe-rich vaginal microbiome has been associated with local inflammation and spontaneous preterm birth (sPTB), but few studies have assessed this association in the setting of HIV. We performed metagenomic sequencing and inflammatory marker assays on vaginal swabs collected in pregnancy. We grouped samples into 7 metagenomic clusters (mgClust) using the non-redundant VIRGO catalogue, and derived inflammatory scores by factor analysis. Of 221 participants, median Shannon diversity index (SDI) was highest in HIV+ with detectable viral load (1.31, IQR: 0.85-1.66; p < 0.001) and HIV+ with undetectable virus (1.17, IQR: 0.51-1.66; p = 0.01) compared to HIV- (0.74, IQR: 0.35-1.26). Inflammatory scores positively correlated with SDI (+ 0.66, 95%CI 0.28, 1.03; p = 0.001), highest among anaerobe-rich mgClust2-mgClust6. HIV was associated with predominance of anaerobe-rich mgClust5 (17% vs. 6%; p = 0.02) and mgClust6 (27% vs. 11%; p = 0.002). Relative abundance of a novel Gardnerella metagenomic subspecies > 50% predicted sPTB (RR 2.6; 95%CI: 1.1, 6.4) and was higher in HIV+ (23% vs. 10%; p = 0.001). A novel Gardnerella metagenomic subspecies more abundant in women with HIV predicted sPTB. The risk of sPTB among women with HIV may be mediated by the vaginal microbiome and inflammation, suggesting potential targets for prevention.

RevDate: 2022-05-20

Dou Q, Zhang L, Lan S, et al (2022)

Metagenomics illuminated the mechanism of enhanced nitrogen removal and vivianite recovery induced by zero-valent iron in partial-denitrification/anammox process.

Bioresource technology pii:S0960-8524(22)00646-0 [Epub ahead of print].

In this study, a novel strategy of zero-valent iron (ZVI) combined with acetic acid was proposed to optimize partial-denitrification/anammox (PD/A) process, and enhanced nitrogen removal mechanism was elucidated through metagenomics. Results showed that the optimal nitrogen and phosphorus removal were as high as 99.50% and 98.37%, respectively, with vivianite being precipitated as the main byproduct. The occurrence of Feammox was a crucial link for enhanced ammonia removal and vivianite recovery. Metagenomic analysis further certified that long-term acclimation of optimization strategy triggered DNRA-based nitrate reducing genes (narY/Z and nrfA) assigned to Candidatus Brocadia, which allow direct uptake of nitrate by the anammox. Additionally, ZVI might act as a new electron donor to decrease organics dependence of PD by reducing the abundance of genes for electron production involved in carbon metabolism. However, FA addition enhanced the relative abundances of genes involved in anammox including nitrogen reduction and oxidation, thereby accelerating nitrogen removal.

RevDate: 2022-05-20

Chen L, Gao X, Xue W, et al (2022)

Rapid metagenomic identification of two major swine pathogens with real-time nanopore sequencing.

Journal of virological methods pii:S0166-0934(22)00092-1 [Epub ahead of print].

Metagenomic next-generation sequencing (mNGS) is a rapid deep-sequencing diagnostic tool for the unbiased identification of pathogens. In this study, we established a nanopore-sequencing-based mNGS protocol to detect two major viral pathogens of swine, Porcine reproductive and respiratory syndrome virus (PRRSV) and Porcine epidemic diarrhea virus (PEDV). Samples were spiked with the serially diluted viruses as standard references to define the specific protocols. The utility of the method was evaluated with key parameters. The limits of detection for PRRSV and PEDV were 2.3 × 102 and 9.0 × 104 copies per reaction, respectively, and good correlations between PCR quantification cycle value and the mapped read count (log value) were observed. Only the nanopore reads could be assembled de novo into nearly full-length of the PRRSV genome, with 99.9% pairwise identity, and 90.0% genome coverage for PEDV. The established protocol was validated in PRRSV-positive clinical samples. The results for PRRSV-positive tissue and serum samples tested with mNGS protocol were 100% concordant with quantitative PCR results. The protocol also recognized infections of single or multiple viruses in a single sample. In conclusion, we have established a nanopore-sequencing-based mNGS protocol that efficiently identifies and characterizes viral pathogen(s) in a variety of clinical sample types.

RevDate: 2022-05-20

Valk LC, Peces M, Singleton CM, et al (2022)

Exploring the microbial influence on seasonal nitrous oxide concentration in a full-scale wastewater treatment plant using metagenome assembled genomes.

Water research, 219:118563 pii:S0043-1354(22)00516-4 [Epub ahead of print].

Nitrous oxide is a highly potent greenhouse gas and one of the main contributors to the greenhouse gas footprint of wastewater treatment plants (WWTP). Although nitrous oxide can be produced by abiotic reactions in these systems, biological N2O production resulting from the imbalance of nitrous oxide production and reduction by microbial populations is the dominant cause. The microbial populations responsible for the imbalance have not been clearly identified, yet they are likely responsible for strong seasonal nitrous oxide patterns. Here, we examined the seasonal nitrous oxide concentration pattern in Avedøre WWTP alongside abiotic parameters, the microbial community composition based on 16S rRNA gene sequencing and already available metagenome-assembled genomes (MAGs). We found that the WWTP parameters could not explain the observed pattern. While no distinct community changes between periods of high and low dissolved nitrous oxide concentrations were determined, we found 26 and 28 species with positive and negative correlations to the seasonal N2O concentrations, respectively. MAGs were identified for 124 species (approximately 31% mean relative abundance of the community), and analysis of their genomic nitrogen transformation potential could explain this correlation for four of the negatively correlated species. Other abundant species were also analysed for their nitrogen transformation potential. Interestingly, only one full-denitrifier (Candidatus Dechloromonas phosphorivorans) was identified. 59 species had a nosZ gene predicted, with the majority identified as a clade II nosZ gene, mainly from the phylum Bacteroidota. A correlation of MAG-derived functional guilds with the N2O concentration pattern showed that there was a small but significant negative correlation with nitrite oxidizing bacteria and species with a nosZ gene (N2O reducers (DEN)). More research is required, specifically long-term activity measurements in relation to the N2O concentration to increase the resolution of these findings.

RevDate: 2022-05-20

Galanis A, Vardakas P, Reczko M, et al (2022)

Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey.

Molecular ecology resources [Epub ahead of print].

Honeybees (Apis mellifera) continue to succumb to human and environmental pressures despite their crucial role in providing essential ecosystem services. Owing to their foraging and honey production activities, honeybees form complex relationships with species across all domains, such as plants, viruses, bacteria and other hive pests, making honey a valuable biomonitoring tool for assessing their ecological niche. Thus, the application of honey shotgun metagenomics (SM) has paved the way for a detailed description of the species honeybees interact with. Nevertheless, SM bioinformatics tools and DNA extraction methods rely on resources not necessarily optimized for honey. In this study, we compared five widely used taxonomic classifiers using simulated species communities commonly found in honey. We found that Kraken 2 with a threshold of 0.5 performs best in assessing species distribution. We also optimized a simple NaOH-based honey DNA extraction methodology (Direct-SM), which profiled species seasonal variability similarly to an established column-based DNA extraction approach (SM). Both approaches produce results consistent with melissopalinology analysis describing the botanical landscape surrounding the apiary. Interestingly, we detected a strong stability of the bacteria constituting the core and noncore gut microbiome across seasons, pointing to the potential utility of honey for noninvasive assessment of bee microbiota. Finally, the Direct-SM approach to detect Varroa correlates well with the biomonitoring of mite infestation observed in hives. These observations suggest that Direct-SM methodology has the potential to comprehensively describe honeybee ecological niches and can be tested as a building block for large-scale studies to assess bee health in the field.

RevDate: 2022-05-20

Wang S, Chen H, Yang H, et al (2022)

Gut Microbiome Was Highly Related to the Regulation of Metabolism in Lung Adenocarcinoma Patients.

Frontiers in oncology, 12:790467.

Background: Lung adenocarcinoma (LUAD) is one of the most predominant subtypes of lung cancer. The gut microbiome plays a vital role in the pathophysiological processes of various diseases, including cancers.

Methods: In the study, 100 individuals were enrolled. In total 75 stool and blood samples were analyzed with 16s-rRNA gene sequencing and metabolomics (30 from healthy individuals (H); 45 from LUAD patients). In addition, 25 stool samples were analyzed with metagenomics (10 from H; 15 from LUAD). The linear discriminant analysis (LDA) effect size (LefSe) and logistic regression analysis were applied to identify biomarkers' taxa and develop a diagnostic model. The diagnostic power of the model was estimated with the receiver operating characteristic curve (ROC) by comparing the area under the ROC (AUC). The correlation between biomarker's taxa and metabolites was calculated using the Spearman analysis.

Results: The α and β diversity demonstrated the composition and structure of the gut microbiome in LUAD patients were different from those in healthy people. The top three abundance of genera were Bacteroides (25.06%), Faecalibacterium (11.00%), and Prevotella (5.94%). The LefSe and logistic regression analysis identified three biomarker taxa (Bacteroides, Pseudomonas, and Ruminococcus gnavus group) and constructed a diagnostic model. The AUCs of the diagnostic model in 16s-rRNA gene sequencing and metagenomics were 0.852 and 0.841, respectively. A total of 102 plasma metabolites were highly related to those three biomarkers' taxa. Seven metabolic pathways were enriched by 102 plasma metabolites, including the Pentose phosphate pathway, Glutathione metabolism.

Conclusions: In LUAD patients, the gut microbiome profile has significantly changed. We used three biomarkers taxa to develop a diagnostic model, which was accurate and suitable for the diagnosis of LUAD. Gut microbes, especially those three biomarkers' taxa, may participate in regulating metabolism-related pathways in LUAD patients, such as the pentose phosphate pathway and glutathione metabolism.

RevDate: 2022-05-20

Guizzo MG, Tirloni L, Gonzalez SA, et al (2022)

Coxiella Endosymbiont of Rhipicephalus microplus Modulates Tick Physiology With a Major Impact in Blood Feeding Capacity.

Frontiers in microbiology, 13:868575.

In the past decade, metagenomics studies exploring tick microbiota have revealed widespread interactions between bacteria and arthropods, including symbiotic interactions. Functional studies showed that obligate endosymbionts contribute to tick biology, affecting reproductive fitness and molting. Understanding the molecular basis of the interaction between ticks and their mutualist endosymbionts may help to develop control methods based on microbiome manipulation. Previously, we showed that Rhipicephalus microplus larvae with reduced levels of Coxiella endosymbiont of R. microplus (CERM) were arrested at the metanymph life stage (partially engorged nymph) and did not molt into adults. In this study, we performed a transcriptomic differential analysis of the R. microplus metanymph in the presence and absence of its mutualist endosymbiont. The lack of CERM resulted in an altered expression profile of transcripts from several functional categories. Gene products such as DA-P36, protease inhibitors, metalloproteases, and evasins, which are involved in blood feeding capacity, were underexpressed in CERM-free metanymphs. Disregulation in genes related to extracellular matrix remodeling was also observed in the absence of the symbiont. Taken together, the observed alterations in gene expression may explain the blockage of development at the metanymph stage and reveal a novel physiological aspect of the symbiont-tick-vertebrate host interaction.

RevDate: 2022-05-20

Noell SE, Baptista MS, Smith E, et al (2022)

Unique Geothermal Chemistry Shapes Microbial Communities on Mt. Erebus, Antarctica.

Frontiers in microbiology, 13:836943.

Mt. Erebus, Antarctica, is the world's southernmost active volcano and is unique in its isolation from other major active volcanic systems and its distinctive geothermal systems. Using 16S rRNA gene amplicon sequencing and physicochemical analyses, we compared samples collected at two contrasting high-temperature (50°C-65°C) sites on Mt. Erebus: Tramway Ridge, a weather-protected high biomass site, and Western Crater, an extremely exposed low biomass site. Samples were collected along three thermal gradients, one from Western Crater and two within Tramway Ridge, which allowed an examination of the heterogeneity present at Tramway Ridge. We found distinct soil compositions between the two sites, and to a lesser extent within Tramway Ridge, correlated with disparate microbial communities. Notably, pH, not temperature, showed the strongest correlation with these differences. The abundance profiles of several microbial groups were different between the two sites; class Nitrososphaeria amplicon sequence variants (ASVs) dominated the community profiles at Tramway Ridge, whereas Acidobacteriotal ASVs were only found at Western Crater. A co-occurrence network, paired with physicochemical analyses, allowed for finer scale analysis of parameters correlated with differential abundance profiles, with various parameters (total carbon, total nitrogen, soil moisture, soil conductivity, sulfur, phosphorous, and iron) showing significant correlations. ASVs assigned to Chloroflexi classes Ktedonobacteria and Chloroflexia were detected at both sites. Based on the known metabolic capabilities of previously studied members of these groups, we predict that chemolithotrophy is a common strategy in this system. These analyses highlight the importance of conducting broader-scale metagenomics and cultivation efforts at Mt. Erebus to better understand this unique environment.

RevDate: 2022-05-20

Borowik A, Wyszkowska J, J Kucharski (2022)

Bacteria and Soil Enzymes Supporting the Valorization of Forested Soils.

Materials (Basel, Switzerland), 15(9): pii:ma15093287.

To decompose forest biomass, microorganisms use specific enzymes from the class of oxidoreductases and hydrolases, which are produced by bacteria and soil fungi. In post-agricultural forest soils, bacteria adapt more easily to changing ecological conditions than fungi. The unique features of bacteria, i.e., tolerance and the ability to degrade a wide range of chemical compounds, prompted us to conduct research that contributes to the improvement of the broadly understood circular management of biomass production and economic efficiency. This study aimed to analyze changes in the microbiological activity and the activities of dehydrogenases, catalase, β-glucosidase, urease, arylsulfatase, acid phosphatase, and alkaline phosphatase in the soil sampled from under Picea abies (Pa), Pinus sylvestris (Ps), Larix decidua (Ld), Quercus robur (Qr), and Betula pendula (Bp), after 19 years. The control object was unforested soil. The studies allowed one to demonstrate the relationship between the activity of soil enzymes and the assemblages of culturable microorganisms and bacteria determined by the metagenomic method and tree species. Thus, it is possible to design the selection of tree species catalyzing enzymatic processes in soil. The strongest growth promoter of microorganisms turned out to be Quercus robur L., followed by Picea abies L., whereas the weakest promoters appeared to be Pinus sylvestris L. and Larix decidua M.

RevDate: 2022-05-19

Thakur M, Kumar Rai A, SP Singh (2022)

An acid-tolerant and cold-active β-galactosidase potentially suitable to process milk and whey samples.

Applied microbiology and biotechnology [Epub ahead of print].

A novel β-galactosidase gene (galM) was cloned from an aquatic habitat metagenome. The analysis of its translated sequence (GalM) revealed its phylogenetic closeness towards Verrucomicrobia sp. The sequence comparison and homology structure analysis designated it a member of GH42 family. The three-dimensional homology model of GalM depicted a typical (β/α)8 TIM-barrel containing the catalytic core. The gene (galM) was expressed in a heterologous host, Escherichia coli, and the purified protein (GalM) was subjected to biochemical characterization. It displayed β-galactosidase activity in a wide range of pH (2.0 to 9.0) and temperature (4 to 60 °C). The heat exposed protein showed considerable stability at 40 and 50 °C, with the half-life of about 100 h and 35 h, respectively. The presence of Na, Mg, K, Ca, and Mn metals was favorable to the catalytic efficiency of GalM, which is a desirable catalytic feature, as these metals exist in milk. It showed remarkable tolerance of glucose and galactose in the reaction. Furthermore, GalM discerned transglycosylation activity that is useful in galacto-oligosaccharides' production. These biochemical properties specify the suitability of this biocatalyst for milk and whey processing applications. KEY POINTS: • A novel β-galactosidase gene was identified and characterized from an aquatic habitat. • It was active in extreme acidic to mild alkaline pH and at cold to moderate temperatures. • The β-galactosidase was capable to hydrolyze lactose in milk and whey.

RevDate: 2022-05-19

Szóstak N, Szymanek A, Havránek J, et al (2022)

The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling.

Scientific reports, 12(1):8470.

In recent years, the number of metagenomic studies increased significantly. Wide range of factors, including the tremendous community complexity and variability, is contributing to the challenge in reliable microbiome community profiling. Many approaches have been proposed to overcome these problems making hardly possible to compare results of different studies. The significant differences between procedures used in metagenomic research are reflected in a variation of the obtained results. This calls for the need for standardisation of the procedure, to reduce the confounding factors originating from DNA isolation, sequencing and bioinformatics analyses in order to ensure that the differences in microbiome composition are of a true biological origin. Although the best practices for metagenomics studies have been the topic of several publications and the main aim of the International Human Microbiome Standard (IHMS) project, standardisation of the procedure for generating and analysing metagenomic data is still far from being achieved. To highlight the difficulties in the standardisation of metagenomics methods, we thoroughly examined each step of the analysis of the human gut microbiome. We tested the DNA isolation procedure, preparation of NGS libraries for next-generation sequencing, and bioinformatics analysis, aimed at identifying microbial taxa. We showed that the homogenisation time is the leading factor impacting sample diversity, with the recommendation for a shorter homogenisation time (10 min). Ten minutes of homogenisation allows for better reflection of the bacteria gram-positive/gram-negative ratio, and the obtained results are the least heterogenous in terms of beta-diversity of samples microbial composition. Besides increasing the homogenisation time, we observed further potential impact of the library preparation kit on the gut microbiome profiling. Moreover, our analysis revealed that the choice of the library preparation kit influences the reproducibility of the results, which is an important factor that has to be taken into account in every experiment. In this study, a tagmentation-based kit allowed for obtaining the most reproducible results. We also considered the choice of the computational tool for determining the composition of intestinal microbiota, with Kraken2/Bracken pipeline outperforming MetaPhlAn2 in our in silico experiments. The design of an experiment and a detailed establishment of an experimental protocol may have a serious impact on determining the taxonomic profile of the intestinal microbiome community. Results of our experiment can be helpful for a wide range of studies that aim to better understand the role of the gut microbiome, as well as for clinical purposes.

RevDate: 2022-05-20
CmpDate: 2022-05-20

Cahan SH, Nguyen AD, Y Zhou (2022)

Population genomics supports multiple hybrid zone origins of socially hybridogenetic lineages of Pogonomyrmex harvester ants.

Evolution; international journal of organic evolution, 76(5):1016-1032.

Reproductive division of labor in the social insects is typically determined by environmental cues; however, genetic effects on caste have been discovered in a growing set of ant taxa. An extreme form of genetic caste determination is "social hybridogenesis," in which co-occurring genetic lineages obligately interbreed to produce workers, whereas daughter queens are of pure-lineage ancestry. In this study, we tested the hypothesis that social hybridogenesis in the genus Pogonomyrmex resulted from one or more interspecific hybridization events, and if so, whether individual lineages were of hybrid ancestry. We reconstructed evolutionary relationships of four lineage pairs to populations of two closely related non-hybridogenetic species, Pogonomyrmex barbatus and Pogonomyrmex rugosus, using nuclear SNP loci and mitochondrial sequencing. The nuclear phylogeny supported a hybridization hypothesis, with one member of each pair nested within P. rugosus, whereas the other was nested within P. barbatus. The source populations corresponded with two distinct geographic areas at the eastern and western edges of a zone of contact. Relatively little gene flow was detected between interbreeding lineages, either historically or currently. This suggests that shifts in reproductive caste determination may reinforce reproductive incompatibility, in a manner similar to the evolution of hybridogenesis in nonsocial systems.

RevDate: 2022-05-19

Mathur Y, Vartak AR, AB Hazra (2022)

Guardian of cobamide diversity: Probing the role of CobT in lower ligand activation in the biosynthesis of vitamin B12 and other cobamide cofactors.

Methods in enzymology, 668:25-59.

Enzymes catalyze a wide variety of reactions with exquisite precision under crowded conditions within cellular environments. When encountered with a choice of small molecules in their vicinity, even though most enzymes continue to be specific about the substrate they pick, some others are able to accept a range of substrates and subsequently produce a variety of products. The biosynthesis of Vitamin B12, an essential nutrient required by humans involves a multi-substrate α-phosphoribosyltransferase enzyme CobT that activates the lower ligand of B12. Vitamin B12 is a member of the cobamide family of cofactors which share a common tetrapyrrolic corrin scaffold with a centrally coordinated cobalt ion, and an upper and a lower ligand. The structural difference between B12 and other cobamides mainly arises from variations in the lower ligand, which is attached to the activated corrin ring by CobT and other downstream enzymes. In this chapter, we describe the steps involved in identifying and reconstituting the activity of new CobT homologs by deriving lessons from those previously characterized. We then highlight biochemical techniques to study the unique properties of these homologs. Finally, we describe a pairwise substrate competition assay to rank CobT substrate preference, a general method that can be applied for the study of other multi-substrate enzymes. Overall, the analysis with CobT provides insights into the range of cobamides that can be synthesized by an organism or a community, complementing efforts to predict cobamide diversity from complex metagenomic data.

RevDate: 2022-05-19

Murali A, Giri V, Cameron HJ, et al (2022)

Investigating the gut microbiome and metabolome following treatment with artificial sweeteners acesulfame potassium and saccharin in young adult Wistar rats.

Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association pii:S0278-6915(22)00321-0 [Epub ahead of print].

To elucidate if artificial sweeteners modify fecal bacterial composition and the fecal and plasma metabolomes, Wistar rats from both sexes were treated for 28 days with acesulfame potassium (40 and 120 mg/kg body weight) and saccharin (20 and 100 mg/kg body weight). Targeted MS-based metabolome profiling (plasma and feces) and fecal 16S gene sequencing were conducted. Both sweeteners exhibited only minor effects on the fecal metabolome and microbiota. Saccharin treatment significantly altered amino acids, lipids, energy metabolism and specifically, bile acids in the plasma metabolome. Additionally, sex-specific differences were observed for conjugated primary and secondary bile acids. Acesulfame potassium treated male rats showed larger alterations in glycine conjugated primary and secondary bile-acids than females. Other changes in the plasma metabolome were more profound for saccharin than acesulfame potassium, for both sexes. Changes in conjugated bile-acids in plasma, which are often associated with microbiome changes, and the absence of similarly large changes in microbiota suggest an adaptative change of the latter, rather than toxicity. Further studies with a high resolution 16S sequencing data and/or metagenomics approach, with particular emphasis on bile acids, will be required to explore the mechanisms driving this metabolic outcome of saccharin in Wistar rats.

RevDate: 2022-05-19

Benyedem H, Lekired A, Mhadhbi M, et al (2022)

First insights into the microbiome of Tunisian Hyalomma ticks gained through next-generation sequencing with a special focus on H. scupense.

PloS one, 17(5):e0268172 pii:PONE-D-21-29206.

Ticks are one of the most important vectors of several pathogens affecting humans and animals. In addition to pathogens, ticks carry diverse microbiota of symbiotic and commensal microorganisms. In this study, we have investigated the first Tunisian insight into the microbial composition of the most dominant Hyalomma species infesting Tunisian cattle and explored the relative contribution of tick sex, life stage, and species to the diversity, richness and bacterial species of tick microbiome. In this regard, next generation sequencing for the 16S rRNA (V3-V4 region) of tick bacterial microbiota and metagenomic analysis were established. The analysis of the bacterial diversity reveals that H. marginatum and H. excavatum have greater diversity than H. scupense. Furthermore, microbial diversity and composition vary according to the tick's life stage and sex in the specific case of H. scupense. The endosymbionts Francisella, Midichloria mitochondrii, and Rickettsia were shown to be the most prevalent in Hyalomma spp. Rickettsia, Francisella, Ehrlichia, and Erwinia are the most common zoonotic bacteria found in Hyalomma ticks. Accordingly, Hyalomma ticks could represent potential vectors for these zoonotic bacterial agents.

RevDate: 2022-05-19

Kohl KD, Dieppa-Colón E, Goyco-Blas J, et al (2022)

Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies.

Integrative and comparative biology pii:6589408 [Epub ahead of print].

The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously. Here, we employed DNA metabarcoding techniques, predictive metagenomics, and culture-dependent techniques to inventory the gut microbial communities of several species of rodent collected from the same environment that employ different natural feeding strategies [granivorous pocket mice (Chaetodipus penicillatus); granivorous kangaroo rats (Dipodomys merriami); herbivorous woodrats (Neotoma albigula); omnivorous cactus mice (Peromyscus eremicus), and insectivorous grasshopper mice (Onychomys torridus)]. Of particular interest were shifts in gut microbial communities in rodent species with herbivorous and insectivorous diets, given the high amounts of indigestible fibers and chitinous exoskeleton in these diets, respectively. We found that herbivorous woodrats harbored the greatest microbial diversity. Granivorous pocket mice and kangaroo rats had the highest abundances of the genus Ruminococcus and highest predicted abundances of genes related to the digestion of fiber, representing potential adaptations in these species to the fiber content of seeds and the limitations to digestion given their small body size. Insectivorous grasshopper mice exhibited the greatest inter-individual variation in the membership of their microbiomes, and also exhibited the highest predicted abundances of chitin-degrading genes. Culture-based approaches identified 178 microbial isolates (primarily Bacillus and Enterococcus) capable of degrading cellulose and chitin. We observed several instances of strain-level diversity in these metabolic capabilities across isolates, somewhat highlighting the limitations and hidden diversity underlying DNA metabarcoding techniques. However, these methods offer power in allowing the investigation of several questions concurrently, thus enhancing our understanding of gut microbial ecology.

RevDate: 2022-05-19

Chen H, Ma K, Lu C, et al (2022)

Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe.

Frontiers in microbiology, 13:878978.

Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient. Our analyses show that soil microbial taxonomic composition varies widely in response to climate and soil physicochemical gradients, while microbial functional attributes based on metagenomic gene abundances are redundant. Among 17 climate zones, microbial taxonomic compositions were more distinct than functional potentials, as climate and edaphic properties showed more significant influence on microbial taxonomic compositions than on functional potentials. Microbial taxonomies formed a larger and more complex co-occurrence network with more module structures than functional potentials. Functional network was strongly inter-connected among different categories, whereas taxonomic network was more positively interactive in the same taxonomic groups. This study provides strong evidence to support the hypothesis of functional redundancy in soil microbes, as microbial taxonomic compositions vary to a larger extent than functional potentials based on metagenomic gene abundances in terrestrial ecosystems across the globe.

RevDate: 2022-05-18

Deng K, Shuai M, Zhang Z, et al (2022)

Temporal relationship among adiposity, gut microbiota, and insulin resistance in a longitudinal human cohort.

BMC medicine, 20(1):171.

BACKGROUND: The temporal relationship between adiposity and gut microbiota was unexplored. Whether some gut microbes lie in the pathways from adiposity to insulin resistance is less clear. Our study aims to reveal the temporal relationship between adiposity and gut microbiota and investigate whether gut microbiota may mediate the association of adiposity with insulin resistance in a longitudinal human cohort study.

METHODS: We obtained repeated-measured gut shotgun metagenomic and anthropometric data from 426 Chinese participants over ~3 years of follow-up. Cross-lagged path analysis was used to examine the temporal relationship between BMI and gut microbial features. The associations between the gut microbes and insulin resistance-related phenotypes were examined using a linear mixed-effect model. We examined the mediation effect of gut microbes on the association between adiposity and insulin resistance-related phenotypes. Replication was performed in the HMP cohort.

RESULTS: Baseline BMI was prospectively associated with levels of ten gut microbial species. Among them, results of four species (Adlercreutzia equolifaciens, Parabacteroides unclassified, Lachnospiraceae bacterium 3 1 57FAA CT1, Lachnospiraceae bacterium 7 1 58FAA) were replicated in the independent HMP cohort. Lachnospiraceae bacterium 3 1 57FAA CT1 was inversely associated with HOMA-IR and fasting insulin. Lachnospiraceae bacterium 3 1 57FAA CT1 mediated the association of overweight/obesity with HOMA-IR (FDR<0.05). Furthermore, Lachnospiraceae bacterium 3 1 57FAA CT1 was positively associated with the butyrate-producing pathway PWY-5022 (p < 0.001).

CONCLUSIONS: Our study identified one potentially beneficial microbe Lachnospiraceae bacterium 3 1 57FAA CT1, which might mediate the effect of adiposity on insulin resistance. The identified microbes are helpful for the discovery of novel therapeutic targets, as to mitigate the impact of adiposity on insulin resistance.

RevDate: 2022-05-18

Yan J, Liao C, Taylor BP, et al (2022)

A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.

Scientific data, 9(1):219.

Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study the human gut microbiome. We previously compiled a large-scale longitudinal dataset of fecal microbiota and associated metadata, but we had limited that analysis to taxonomic composition of bacteria from 16S rRNA gene sequencing. Here we augment those data with shotgun metagenomics. The compilation amounts to a nested subset of 395 samples compiled from different studies at Memorial Sloan Kettering. Shotgun metagenomics describes the microbiome at the functional level, particularly in antimicrobial resistances and virulence factors. We provide accession numbers that link each sample to the paired-end sequencing files deposited in a public repository, which can be directly accessed by the online services of PATRIC to be analyzed without the users having to download or transfer the files. Then, we show how shotgun sequencing enables the assembly of genomes from metagenomic data. The new data, combined with the metadata published previously, enables new functional studies of the microbiomes of patients with cancer receiving bone marrow transplantation.

RevDate: 2022-05-19
CmpDate: 2022-05-19

Schriml LM (2022)

A decade of GigaScience: 10 years of the evolving genomic and biomedical standards landscape.

GigaScience, 11:.

Standardization of omics data drives FAIR data practices through community-built genomic data standards and biomedical ontologies. Use of standards has progressed from a foreign concept to a sought-after solution, moving from efforts to coordinate data within individual research projects to research communities coming together to identify solutions to common challenges. Today we are seeing the benefits of this multidecade groundswell to coordinate, exchange, and reuse data; to compare data across studies; and to integrate data across previously siloed resources.

RevDate: 2022-05-18

He T, Zhu C, Li Z, et al (2022)

Virome analysis of ticks in Zhoushan Archipelago, China.

The Journal of veterinary medical science [Epub ahead of print].

Ticks are an important group of arthropod vectors. Ticks pose a profound risk to public health by transmitting many types of microorganisms that are human and animal pathogens. With the development of next-generation sequencing (NGS) technology and viral metagenomics, numerous novel viruses have been discovered in ticks and tick-related hosts. To fully understand the virus spectrum in ticks in the Zhoushan Archipelago of Zhejiang province in China, ticks were collected from Qushan Island, Zhoushan Island, and Daishan Island in the Zhoushan Archipelago in June 2016. NGS performed to investigate the diversity of tick-associated viruses identified 21 viral sequences. Twelve were pathogenic to humans and animals. Trough verification by polymerase chain reaction (PCR) revealed the existence of three tick-associated viruses with extensive homology with Dabieshan, MG22, and Odaw virus. Other NGS-detected sequences that could not be amplified by PCR were highly homologous (92-100%) with known pathogenic viruses that included hepatitis B virus, papillomavirus, and human mastadenovirus C. This is the first study to systematically apply high throughput sequencing technology to explore the spectrum of viruses carried by ticks in the Zhoushan Archipelago. The findings are fundamental knowledge of the diversity of tick-associated viruses in this region and will inform strategies to monitor and prevent the spread of tick-borne diseases.

RevDate: 2022-05-18

Koskella B, Hernandez CA, RM Wheatley (2022)

Understanding the Impacts of Bacteriophage Viruses: From Laboratory Evolution to Natural Ecosystems.

Annual review of virology [Epub ahead of print].

Viruses of bacteriophages (phages) have broad effects on bacterial ecology and evolution in nature that mediate microbial interactions, shape bacterial diversity, and influence nutrient cycling and ecosystem function. The unrelenting impact of phages within the microbial realm is the result, in large part, of their ability to rapidly evolve in response to bacterial host dynamics. The knowledge gained from laboratory systems, typically using pairwise interactions between single-host and single-phage systems, has made clear that phages coevolve with their bacterial hosts rapidly, somewhat predictably, and primarily by counteradapting to host resistance. Recent advancement in metagenomics approaches, as well as a shifting focus toward natural microbial communities and host-associated microbiomes, is beginning to uncover the full picture of phage evolution and ecology within more complex settings. As these data reach their full potential, it will be critical to ask when and how insights gained from studies of phage evolution in vitro can be meaningfully applied to understanding bacteria-phage interactions in nature. In this review, we explore the myriad ways that phages shape and are themselves shaped by bacterial host populations and communities, with a particular focus on observed and predicted differences between the laboratory and complex microbial communities. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

RevDate: 2022-05-18

Singh R, Pal DB, Alkhanani MF, et al (2022)

Prospects of soil microbiome application for lignocellulosic biomass degradation: An overview.

The Science of the total environment pii:S0048-9697(22)03063-7 [Epub ahead of print].

Sustainable and practically viable biofuels production technology using lignocellulosic biomass is still seeking its way of implementation owing to some major issues involved therein. Unavailability of efficient microbial sources for the degradation of cellulosic biomass is one of the major roadblocks in biomass to biofuels production technology. In this context, utilization of microbiomes to degrade lignocellulaosic biomass is emerging as a rapid and effective approach that can fulfill the requirements of biomass based biofuels production technology. Therefore, the present review is targeted to explore soil metagenomic approach to improve the lignocellulosic biomass degradation processing for the cost-effective and eco-friendly application. Soil microbiomes consist of rich microbial community along with high probability of cellulolytic microbes, and can be identified by culture independent metagenomics method which can be structurally and functionally explored via genomic library. Therefore, in depth analysis and discussion have also been made via structural & functional metagenomics tools along with their contribution to genomic library. Additionally, the present review highlights currently existing bottlenecks along with their feasible solutions. This review will help to understand the basic research as well as industrial concept for the process improvement based on soil microbiome mediated lignocellulosic biomass degradation, and this may likely to implement for the low-cost commercial biofuels production technology.

RevDate: 2022-05-18

Kuroda K, Narihiro T, Shinshima F, et al (2022)

High-rate cotreatment of purified terephthalate and dimethyl terephthalate manufacturing wastewater by a mesophilic upflow anaerobic sludge blanket reactor and the microbial ecology relevant to aromatic compound degradation.

Water research, 219:118581 pii:S0043-1354(22)00534-6 [Epub ahead of print].

Polyethylene terephthalate (PET) is produced worldwide, mainly as material for plastic drink bottles. PET is produced by polymerization of purified terephthalate (PTA) or dimethyl terephthalate (DMT) with ethylene glycol. During the synthetic manufacturing processes of PTA and DMT, high organic loading wastewater is produced, which is typically treated separately by anaerobic wastewater treatment technologies. Given the high demand for PET, manufacturing plants are expanding globally, which will result in an increase in the amounts of PTA and DMT wastewater in need of treatment. In terms of effective treatment, the cotreatment of PTA and DMT wastewater has several advantages, including lower area and energy requirements. In this study, we examined the performance of an upflow anaerobic sludge blanket (UASB) reactor in cotreating PTA and DMT wastewater with high organic loading, evaluating its removal characteristics after 518 days of continuous operation. In addition, we performed a microbiome analysis of the UASB granular sludge to uncover the microbial interactions and metabolic functions within the reactor. By continuous operation, we achieved an organic removal rate of 6.6 kg m-3 day-1. In addition, we confirmed that aromatic compounds in the complex wastewater from the PTA and DMT manufacturing processes are biodegradable in the following order: benzoate > orthophthalate > terephthalate > isophthalate > p-toluic acid. 16S rRNA gene-based network analysis shows that anaerobic Woesearchaeales belonging to phylum Nanoarchaeota has a positive correlation with Methanoregula, Candidatus Methanofastidiosum, and Methanosarcina, suggesting a symbiotic relationship with methanogens in granular sludge. Shotgun metagenomic analysis revealed that terephthalate, isophthalate/orthophthalate, and benzoate were degraded by different members of Pelotomaculaceae and Syntrophorhabdaceae. According to the genomic information, we propose two new possible routes for orthophthalate degradation by the Syntrophorhabdaceae organism.

RevDate: 2022-05-18

Han W, Tang H, Y Ye (2022)

Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype.

Journal of computational biology : a journal of computational molecular cell biology [Epub ahead of print].

Microbial organisms play important roles in many aspects of human health and diseases. Encouraged by the numerous studies that show the association between microbiomes and human diseases, computational and machine learning methods have been recently developed to generate and utilize microbiome features for prediction of host phenotypes such as disease versus healthy cancer immunotherapy responder versus nonresponder. We have previously developed a subtractive assembly approach, which focuses on extraction and assembly of differential reads from metagenomic data sets that are likely sampled from differential genomes or genes between two groups of microbiome data sets (e.g., healthy vs. disease). In this article, we further improved our subtractive assembly approach by utilizing groups of k-mers with similar abundance profiles across multiple samples. We implemented a locality-sensitive hashing (LSH)-enabled approach (called kmerLSHSA) to group billions of k-mers into k-mer coabundance groups (kCAGs), which were subsequently used for the retrieval of differential kCAGs for subtractive assembly. Testing of the kmerLSHSA approach on simulated data sets and real microbiome data sets showed that, compared with the conventional approach that utilizes all genes, our approach can quickly identify differential genes that can be used for building promising predictive models for microbiome-based host phenotype prediction. We also discussed other potential applications of LSH-enabled clustering of k-mers according to their abundance profiles across multiple microbiome samples.

RevDate: 2022-05-18

Johnson MA, Liu H, Bush E, et al (2022)

Investigating plant disease outbreaks with long-read metagenomics: sensitive detection and highly resolved phylogenetic reconstruction applied to Xylella fastidiosa.

Microbial genomics, 8(5):.

Early disease detection is a prerequisite for enacting effective interventions for disease control. Strains of the bacterial plant pathogen Xylella fastidiosa have recurrently spread to new crops in new countries causing devastating outbreaks. So far, investigation of outbreak strains and highly resolved phylogenetic reconstruction have required whole-genome sequencing of pure bacterial cultures, which are challenging to obtain due to the fastidious nature of X. fastidiosa. Here, we show that culture-independent metagenomic sequencing, using the Oxford Nanopore Technologies MinION long-read sequencer, can sensitively and specifically detect the causative agent of Pierce's disease of grapevine, X. fastidiosa subspecies fastidiosa. Using a DNA sample from a grapevine in Virginia, USA, it was possible to obtain a metagenome-assembled genome (MAG) of sufficient quality for phylogenetic reconstruction with SNP resolution. The analysis placed the MAG in a clade with isolates from Georgia, USA, suggesting introduction of X. fastidiosa subspecies fastidiosa to Virginia from the south-eastern USA. This proof of concept study, thus, revealed that metagenomic sequencing can replace culture-dependent genome sequencing for reconstructing transmission routes of bacterial plant pathogens.

RevDate: 2022-05-18

Zhao F, Wang C, Song S, et al (2022)

Intake of a chicken protein-based or soy protein-based diet differentially affects growth performance, absorptive capacity, and gut microbiota in young rats.

Molecular nutrition & food research [Epub ahead of print].

SCOPE: Both plant and animal products provide protein for human demands. However, the effect of protein sources on the physiological responses and the composition and functions of gut microbiota during the early stage of life have received little attention.

METHODS AND RESULTS: In the present study, chicken protein and soy protein were fed to young weaning rats for 14 days based on the AIN-93G diet formulation. The growth performance was recorded, and the morphology of the small intestine was analyzed to estimate the absorptive capacity. Shotgun metagenomic sequencing was applied to analyze the cecal microbiota. The chicken protein-based diet enhanced growth performance and absorptive capacity in young rats compared to the soy protein-based diet. The chicken protein-based diet maintained higher levels of Lactobacillus species, associated with glutathione synthesis.

CONCLUSION: The chicken protein-based diet seems favorable for young growing rats in relation to growth performance and absorptive capacity, correlated with changes in the composition and functional potential of the gut microbiota. This article is protected by copyright. All rights reserved.

RevDate: 2022-05-18

Marini S, Oliva M, Slizovskiy IB, et al (2022)

AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data.

GigaScience, 11:.

BACKGROUND: Antimicrobial resistance (AMR) is a global health concern. High-throughput metagenomic sequencing of microbial samples enables profiling of AMR genes through comparison with curated AMR databases. However, the performance of current methods is often hampered by database incompleteness and the presence of homology/homoplasy with other non-AMR genes in sequenced samples.

RESULTS: We present AMR-meta, a database-free and alignment-free approach, based on k-mers, which combines algebraic matrix factorization into metafeatures with regularized regression. Metafeatures capture multi-level gene diversity across the main antibiotic classes. AMR-meta takes in reads from metagenomic shotgun sequencing and outputs predictions about whether those reads contribute to resistance against specific classes of antibiotics. In addition, AMR-meta uses an augmented training strategy that joins an AMR gene database with non-AMR genes (used as negative examples). We compare AMR-meta with AMRPlusPlus, DeepARG, and Meta-MARC, further testing their ensemble via a voting system. In cross-validation, AMR-meta has a median f-score of 0.7 (interquartile range, 0.2-0.9). On semi-synthetic metagenomic data-external test-on average AMR-meta yields a 1.3-fold hit rate increase over existing methods. In terms of run-time, AMR-meta is 3 times faster than DeepARG, 30 times faster than Meta-MARC, and as fast as AMRPlusPlus. Finally, we note that differences in AMR ontologies and observed variance of all tools in classification outputs call for further development on standardization of benchmarking data and protocols.

CONCLUSIONS: AMR-meta is a fast, accurate classifier that exploits non-AMR negative sets to improve sensitivity and specificity. The differences in AMR ontologies and the high variance of all tools in classification outputs call for the deployment of standard benchmarking data and protocols, to fairly compare AMR prediction tools.

RevDate: 2022-05-18

Santoro D, Pellegrina L, Comin M, et al (2022)

SPRISS: Approximating Frequent K-mers by Sampling Reads, and Applications.

Bioinformatics (Oxford, England) pii:6588068 [Epub ahead of print].

MOTIVATION: The extraction of k-mers is a fundamental component in many complex analyses of large next-generation sequencing datasets, including reads classification in genomics and the characterization of RNA-seq datasets. The extraction of all k-mers and their frequencies is extremely demanding in terms of running time and memory, owing to the size of the data and to the exponential number of k-mers to be considered. However, in several applications, only frequent k-mers, which are k-mers appearing in a relatively high proportion of the data, are required by the analysis.

RESULTS: In this work we present SPRISS, a new efficient algorithm to approximate frequent k-mers and their frequencies in next-generation sequencing data. SPRISS employs a simple yet powerful reads sampling scheme, which allows to extract a representative subset of the dataset that can be used, in combination with any k-mer counting algorithm, to perform downstream analyses in a fraction of the time required by the analysis of the whole data, while obtaining comparable answers. Our extensive experimental evaluation demonstrates the efficiency and accuracy of SPRISS in approximating frequent k-mers, and shows that it can be used in various scenarios, such as the comparison of metagenomic datasets, the identification of discriminative k-mers, and SNP (single nucleotide polymorphism) genotyping, to extract insights in a fraction of the time required by the analysis of the whole dataset.

AVAILABILITY: SPRISS* is available at https://github.com/VandinLab/SPRISS.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2022-05-18

Hu D, X Zhao (2022)

Characterization of a New Xylanase Found in the Rumen Metagenome and Its Effects on the Hydrolysis of Wheat.

Journal of agricultural and food chemistry [Epub ahead of print].

Wheat is the main ingredient of poultry diet, but its xylan has an adverse impact on poultry production. A novel xylanase from beef cattle rumen metagenome (RuXyn) and its effect on the wheat hydrolysis were investigated in the present study. The RuXyn coded for 377 amino acids and exhibited low identity (<40%) to previously reported proteins. The RuXyn was heterologously expressed in Escherichia coli and showed maximum activity at pH 6.0 and 40 °C. The activity of RuXyn could be increased by 79.8 and 36.0% in the presence of Ca2+ and Tween 20, respectively. The soluble xylan and insoluble xylan in wheat could be effectively degraded by RuXyn and xylooligosaccharides produced accounting for more than 80% of the products. This study demonstrates that RuXyn has substantial potential to improve the application of wheat in poultry production by degrading wheat xylan and the accompanying xylooligosaccharides produced.

RevDate: 2022-05-18

Zhang CF, Fang XY, Huang ZD, et al (2022)

Surgical Management for Chronic Destructive Septic Hip Arthritis: Debridement, Antibiotics, and Single-Stage Replacement is as Effective as Two-Stage Arthroplasty.

Orthopaedic surgery [Epub ahead of print].

OBJECTIVE: To compare the surgical outcomes of debridement, antibiotics, and single-stage total hip replacement (DASR) vs two-stage arthroplasty (two-stage arthroplasty) for chronic destructive septic hip arthritis (SHA).

METHODS: Cases of chronic destructive SHA treated by DASR or two-stage arthroplasty in our department from January 2008 to October 2021 were retrospectively reviewed. Patient demographic information, perioperative inflammation markers, intraoperative blood loss, microbial culture, and metagenomic new generation sequencing results were recorded. The perioperative complications, hospital stay, hospitalization cost, infection recurrence rate, and Harris Hip Score (HHS) at the last follow-up were compared between the two groups.

RESULTS: A total of 28 patients were included in the study, including 11 patients who received DASR and 17 patients who received two-stage arthroplasty. There was no significant difference in demographic information, preoperative serum inflammatory markers, synovial fluid white blood cell count, or percentage of polymorphonuclear leukocytes between the two groups. The DASR group demonstrated significantly lower intraoperative blood loss [(368.2 ± 253.3) mL vs (638.2 ± 170.0) mL, p = 0.002], hospital stay [(22.6 ± 8.1) days vs (43.5 ± 13.2) days, p < 0.0001], and hospitalization expenses [(81,269 ± 11,496) RMB vs (137,524 ± 25,516) RMB, p < 0.0001] than the two-stage arthroplasty group. In the DASR group, one patient had dislocation as a complication. There were no cases with recurrence of infection. In the two-stage arthroplasty group, there was one case complicated with spacer fracture, one case with spacer dislocation, and one case with deep vein thrombosis of the lower limbs. There were no cases with recurrence of infection. There were no significant differences in the readmission rate, complication rate, or HHS at the last follow-up between the two groups.

CONCLUSIONS: Both DASR and two-stage arthroplasty achieved a satisfactory infection cure rate and functional recovery for chronic destructive SHA, and DASR demonstrated significantly lower intraoperative blood loss, hospital stay, and hospitalization costs than two-stage arthroplasty. For appropriately indicated patients, if microbial data are available and a standardized debridement protocol is strictly followed, DASR can be a treatment option.

RevDate: 2022-05-17

Rajabi M, Nourisanami F, Ghadikolaei KK, et al (2022)

Metagenomic psychrohalophilic xylanase from camel rumen investigated for bioethanol production from wheat bran using Bacillus subtilis AP.

Scientific reports, 12(1):8152.

Bioethanol produced from lignocellulosic biomass is regarded as a clean and sustainable energy source. The recalcitrant structure of lignocellulose is a major drawback to affordable bioethanol production from plant biomass. In this study, a novel endo-1,4-xylanase, named Xyn-2, from the camel rumen metagenome, was characterized and evaluated for hydrolysis of agricultural wastes. The enzyme was identified as a psychrohalophilic xylanase with maximum activity at 20 °C, keeping 58% of the activity at 0 °C, and exhibiting twice as much activity in 0.5-4 M NaCl concentrations. Xyn-2 was able to hydrolyze wheat bran (100%), sunflower-seed shell (70%), wheat straw (56%), rice straw (56%), and rice bran (41%), in the relative order of efficiency. Besides, the ethanologenic B. subtilis AP was evaluated without and with Xyn-2 for bioethanol production from wheat bran. The strain was able to produce 5.5 g/L ethanol with a yield of 22.6% in consolidated bioprocessing (CBP). The contribution of Xyn-2 to ethanol production of B. subtilis AP was studied in an SSF system (simultaneous saccharification and fermentation) giving rise to a significant increase in ethanol production (p ≤ 0.001) to a final concentration of 7.3 g/L with a yield of 26.8%. The results revealed that the camel rumen metagenome might be an invaluable source of novel xylanolytic enzymes with potential application in lignocellulosic biomass valorization. At the same time, the results suggest that B. subtilis with a diverse carbon-source preference and sophisticated systems for production and secretion of enzymes might be a promising candidate for strain development for bioethanol production from plant biomass. It might be assumed that the fortification of B. subtilis enzymatic arsenal with select xylanolytic enzymes from camel rumen metagenome may have a great impact on bioethanol production.

RevDate: 2022-05-17

Johny TK, Puthusseri RM, Saidumohamed BE, et al (2022)

Appraisal of cytotoxicity and acrylamide mitigation potential of L-asparaginase SlpA from fish gut microbiome.

Applied microbiology and biotechnology [Epub ahead of print].

L-asparaginase catalyzes the hydrolysis of L-asparagine to L-aspartic acid and ammonia. It has application in the treatment of acute lymphoblastic leukemia in children, as well as in other malignancies, in addition to its role as a food processing aid for the mitigation of acrylamide formation in the baking industry. Its use in cancer chemotherapy is limited due to problems such as its intrinsic glutaminase activity and associated side effects, leading to an increased interest in the search for novel L-asparaginases without L-glutaminase activity. This study reports the cloning and expression of an L-asparaginase contig obtained from whole metagenome shotgun sequencing of Sardinella longiceps gut microbiota. Purified recombinant glutaminase-free L-asparaginase SlpA was a 74 kDa homodimer, with maximal activity at pH 8 and 30 °C. Km and Vmax of SlpA were determined to be 3.008 mM and 0.014 mM/min, respectively. SlpA displayed cytotoxic activity against K-562 (chronic myeloid leukemia) and MCF-7 (breast cancer) cell lines with IC50 values of 0.3443 and 2.692 U/mL, respectively. SlpA did not show any cytotoxic activity against normal lymphocytes and was proved to be hemocompatible. Pre-treatment of biscuit and bread dough with different concentrations of SlpA resulted in a clear, dose-dependent reduction of acrylamide formation during baking. KEY POINTS: • Cloned and expressed L-asparaginase (SlpA) from fish gut microbiota • Purified SlpA displayed good cytotoxicity against K-562 and MCF-7 cell lines • SlpA addition caused a significant reduction of acrylamide formation during baking.

RevDate: 2022-05-18

Sim M, Lee J, Wy S, et al (2022)

Generation and application of pseudo-long reads for metagenome assembly.

GigaScience, 11:.

BACKGROUND: Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and challenging task because mixed genomes of multiple microorganisms constitute the metagenome. Although long read sequencing technologies have been developed and have begun to be used for metagenomic assembly, many metagenomic studies have been performed based on short reads because the generation of long reads requires higher sequencing cost than short reads.

RESULTS: In this study, we present a new method called PLR-GEN. It creates pseudo-long reads from metagenomic short reads based on given reference genome sequences by considering small sequence variations existing in individual genomes of the same or different species. When applied to a mock community data set in the Human Microbiome Project, PLR-GEN dramatically extended short reads in length of 101 bp to pseudo-long reads with N50 of 33 Kbp and 0.4% error rate. The use of these pseudo-long reads generated by PLR-GEN resulted in an obvious improvement of metagenomic assembly in terms of the number of sequences, assembly contiguity, and prediction of species and genes.

CONCLUSIONS: PLR-GEN can be used to generate artificial long read sequences without spending extra sequencing cost, thus aiding various studies using metagenomes.

RevDate: 2022-05-17

Bommana S, Richards G, Kama M, et al (2022)

Metagenomic Shotgun Sequencing of Endocervical, Vaginal, and Rectal Samples among Fijian Women with and without Chlamydia trachomatis Reveals Disparate Microbial Populations and Function across Anatomic Sites: a Pilot Study.

Microbiology spectrum [Epub ahead of print].

Chlamydia trachomatis is a sexually transmitted pathogen and a global public health concern. Little is known about the microbial composition and function across endocervical, vaginal, and rectal microbiomes in the context of C. trachomatis infection. We evaluated the microbiomes of 10 age-matched high-risk Fijian women with and without C. trachomatis using metagenomic shotgun sequencing (MSS). Lactobacillus iners and Lactobacillus crispatus dominated the vagina and endocervix of uninfected women. Species often found in higher relative abundance in bacterial vaginosis (BV)-Mageeibacillus indolicus, Prevotella spp., Sneathia spp., Gardnerella vaginalis, and Veillonellaceae spp.-were dominant in C. trachomatis-infected women. This combination of BV pathogens was unique to Pacific Islanders compared to previously studied groups. The C. trachomatis-infected endocervix had a higher diversity of microbiota and microbial profiles that were somewhat different from those of the vagina. However, community state type III (CST-III) and CST-IV predominated, reflecting pathogenic microbiota regardless of C. trachomatis infection status. Rectal microbiomes were dominated by Prevotella and Bacteroides, although four women had unique microbiomes with Gardnerella, Akkermansia, Bifidobacterium, and Brachyspira. A high level of microbial similarity across microbiomes in two C. trachomatis-infected women suggested intragenitorectal transmission. A number of metabolic pathways in the endocervix, driven by BV pathogens and C. trachomatis to meet nutritional requirements for survival/growth, 5-fold higher than that in the vagina indicated that endocervical microbial functions are likely more diverse and complex than those in the vagina. Our novel findings provide the impetus for larger prospective studies to interrogate microbial/microbiome interactions that promote C. trachomatis infection and better define the unique genitorectal microbiomes of Pacific Islanders. IMPORTANCE Chlamydia trachomatis is the primary cause of bacterial sexually transmitted infections worldwide, with a disturbing increase in annual rates. While there is a plethora of data on healthy and pathogenic vaginal microbiomes-defining microbial profiles and associations with sexually transmitted infections (STIs)-far fewer studies have similarly examined the endocervix or rectum. Further, vulnerable populations, such as Pacific Islanders, remain underrepresented in research. We investigated the microbial composition, structure, and function of these anatomic microbiomes using metagenomic shotgun sequencing among a Fijian cohort. We found, primarily among C. trachomatis-infected women, unique microbial profiles in endocervical, vaginal, and rectal microbiomes with an increased diversity and more complex microbial pathways in endocervical than vaginal microbiomes. Similarities in microbiome composition across sites for some women suggested intragenitorectal transmission. These novel insights into genitorectal microbiomes and their purported function require prospective studies to better define Pacific Islander microbiomes and microbial/microbiome interactions that promote C. trachomatis infection.

RevDate: 2022-05-17

Devi P, Maurya R, Mehta P, et al (2022)

Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome.

Microbiology spectrum [Epub ahead of print].

The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and Halomonas sp. in the mild COVID-19 patients. Additionally, the metabolic pathways, distinguishing the microbial functional signatures between the clinical sub-phenotypes, were also identified. We report a plausible mechanism wherein the increased transcriptionally active bacterial isolates might contribute to enhanced inflammatory response and co-infections that could modulate the disease severity in these groups. Current study provides an opportunity for potentially using these bacterial species for screening and identifying COVID-19 patient sub-groups with severe disease outcome and priority medical care. IMPORTANCE COVID-19 is invariably a disease of diverse clinical manifestation, with multiple facets involved in modulating the progression and outcome. In this regard, we investigated the role of transcriptionally active microbial co-infections as possible modulators of disease pathology in hospital admitted SARS-CoV-2 infected patients. Specifically, can there be early nasopharyngeal microbial signatures indicative of prospective disease severity? Based on disease severity symptoms, the patients were segregated into clinical sub-phenotypes: mild, moderate, severe (recovered), and mortality. We identified significant presence of transcriptionally active isolates, Achromobacter xylosoxidans and Bacillus cereus in the mortality patients. Importantly, the bacterial species might contribute toward enhancing the inflammatory responses as well as reported to be resistant to common antibiotic therapy, which together hold potential to alter the disease severity and outcome.

RevDate: 2022-05-17

Tanabe TS, C Dahl (2022)

HMS-S-S: a tool for the identification of sulfur metabolism-related genes and analysis of operon structures in genome and metagenome assemblies.

Molecular ecology resources [Epub ahead of print].

Sulfur compounds are used in a variety of biological processes including respiration and photosynthesis. Sulfide and sulfur compounds of intermediary oxidation state can serve as electron donors for lithotrophic growth while sulfate, thiosulfate and sulfur are used as electron acceptors in anaerobic respiration. The biochemistry underlying the manifold transformations of inorganic sulfur compounds occurring in sulfur metabolizing prokaryotes is astonishingly complex and knowledge about it has immensely increased over the last years. The advent of next-generation sequencing approaches as well as the significant increase of data availability in public databases has driven focus of environmental microbiology to probing the metabolic capacity of microbial communities by analysis of this sequence data. To facilitate these analyses, we created HMS-S-S, a comprehensive equivalogous hidden Markov model (HMM)-supported tool. Protein sequences related to sulfur compound oxidation, reduction, transport and intracellular transfer are efficiently detected and related enzymes involved in dissimilatory sulfur oxidation as opposed to sulfur compound reduction can be confidently distinguished. HMM search results are coupled to corresponding genes, which allows analysis of co-occurrence, synteny and genomic neighborhood. The HMMs were validated on an annotated test dataset and by cross-validation. We also proved its performance by exploring meta-assembled genomes isolated from samples from environments with active sulfur cycling, including members of the cable bacteria, novel Acidobacteria and assemblies from a sulfur-rich glacier, and were able to replicate and extend previous reports.

RevDate: 2022-05-16

Gao M, Yang J, Liu Y, et al (2022)

Deep insights into the anaerobic co-digestion of waste activated sludge with concentrated leachate under different salinity stresses.

The Science of the total environment pii:S0048-9697(22)03019-4 [Epub ahead of print].

Treatment of high-salinity organic wastewater (e.g., concentrated leachate) is a major challenge. Anaerobic co-digestion can effectively treat high-salinity organic wastewater and recover energy. In this study, the concentrated landfill leachate and waste activated sludge (WAS) were anaerobic co-digested in the lab-scale continuous stirred tank reactors (CSTR) to understand their co-digestion performance under different salinity stresses. As revealed by the results, when the salinity was low (<10 g/L), the removal ratio of organic matter in the digester was kept at a high level (>91.3%), and the concentration of total volatile fatty acids (TVFAs) was low (<100 mg COD/L), indicating that the digester could operate efficiently and stably. However, when the salinity level was elevated from 10 g/L to 30 g/L, the removal ratio of organic matter in the digester decreased from ~91.3% to ~64.5%, the TVFAs continued to accumulate, the yields of biogas and methane also dropped sharply, and the performance of the digester decreased gradually. The results of microbial community and diversity analysis showed that there is limited adaptability of microbial community to high salinity in such process. Salinity could cause significant changes in the microbial community and diversity, thereby affecting the digestive performance. Metagenomic analysis showed that under high salinity conditions, the content of genes encoding hydrolase and methanogenic enzyme decreased, whereas the pathway of acetotrophic methanogenesis was weakened. Mechanism study showed that with the increase of salinity, the activity of microbial cells decreased, the structure of sludge flocs was damaged more significantly, and the extracellular polymeric substances (EPS) secreted by microbe increased continuously, which was used to resist the toxic effects of salinity stresses on microorganisms. The results of this study could provide certain theoretical guidance for anaerobic digestion under salinity stresses.

RevDate: 2022-05-19

Calderón-Franco D, Sarelse R, Christou S, et al (2022)

Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant.

Water research, 219:118571 pii:S0043-1354(22)00524-3 [Epub ahead of print].

In the One Health context, wastewater treatment plants (WWTPs) are central to safeguarding water resources. Nonetheless, many questions remain about their effectiveness in preventing antimicrobial resistance (AMR) dissemination. Most surveillance studies monitor the levels and removal of selected antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in intracellular DNA (iDNA) extracted from WWTP influents and effluents. The role of extracellular free DNA (exDNA) in wastewater is mostly overlooked. This study analyzed the transfer of ARGs and MGEs in a full-scale Nereda® reactor removing nutrients with aerobic granular sludge. We tracked the composition and fate of the iDNA and exDNA pools of influent, sludge, and effluent samples. Metagenomics was used to profile the microbiome, resistome, and mobilome signatures of iDNA and exDNA extracts. Selected ARGs and MGEs were analyzed by qPCR. From 2,840 ARGs identified, the genes arr-3 (2%), tetC (1.6%), sul1 (1.5%), oqxB (1.2%), and aph(3")-Ib (1.2%) were the most abundant among all sampling points and bioaggregates. Pseudomonas, Acinetobacter, Aeromonas, Acidovorax, Rhodoferax, and Streptomyces populations were the main potential hosts of ARGs in the sludge. In the effluent, 478 resistance determinants were detected, of which 89% were from exDNA potentially released by cell lysis during aeration in the reactor. MGEs and multiple ARGs were co-localized on the same extracellular genetic contigs. Total intracellular ARGs decreased 3-42% due to wastewater treatment. However, the ermB and sul1 genes increased by 2 and 1 log gene copies mL-1, respectively, in exDNA from influent to effluent. The exDNA fractions need to be considered in AMR surveillance, risk assessment, and mitigation strategies.

RevDate: 2022-05-16

Zhao F, Lauder K, Liu S, et al (2022)

Chemoenzymatic Cascades for the Enantioselective Synthesis of β-Hydroxysulfides Bearing a Stereocentre at C- O or C - S Bonds by Ketoreductases (KREDs).

Angewandte Chemie (International ed. in English) [Epub ahead of print].

Chiral β-hydroxysulfides are an important class of organic compounds which find broad application in organic and pharmaceutical chemistry. Herein we describe the development of novel biocatalytic and chemoenzymatic methods for the enantioselective synthesis of β-hydroxysulfides by exploiting ketoreductase (KRED) enzymes. Four KREDs were discovered from a pool of 384 enzymes identified and isolated through a metagenomic approach. KRED311 and KRED349 catalysed the synthesis of β-hydroxysulfides bearing a stereocentre at the C-O bond with opposite absolute configurations and excellent ee values by novel chemoenzymatic and biocatalytic-chemical-biocatalytic (bio-chem-bio) cascades starting from commercially available thiophenols/thiols and α-haloketones/alcohols. KRED253 and KRED384 catalysed the enantioselective synthesis of β-hydroxysulfides bearing a stereocentre at the C-S bond with opposite enantioselectivities by dynamic kinetic resolution (DKR) of racemic α-thioaldehydes.

RevDate: 2022-05-16

Bennett AC, Murugapiran SK, Kees ED, et al (2022)

Temperature and Geographic Location Impact the Distribution and Diversity of Photoautotrophic Gene Variants in Alkaline Yellowstone Hot Springs.

Microbiology spectrum [Epub ahead of print].

Alkaline hot springs in Yellowstone National Park (YNP) provide a framework to study the relationship between photoautotrophs and temperature. Previous work has focused on studying how cyanobacteria (oxygenic phototrophs) vary with temperature, sulfide, and pH, but many questions remain regarding the ecophysiology of anoxygenic photosynthesis due to the taxonomic and metabolic diversity of these taxa. To this end, we examined the distribution of genes involved in phototrophy, carbon fixation, and nitrogen fixation in eight alkaline (pH 7.3-9.4) hot spring sites near the upper temperature limit of photosynthesis (71ºC) in YNP using metagenome sequencing. Based on genes encoding key reaction center proteins, geographic isolation plays a larger role than temperature in selecting for distinct phototrophic Chloroflexi, while genes typically associated with autotrophy in anoxygenic phototrophs, did not have distinct distributions with temperature. Additionally, we recovered Calvin cycle gene variants associated with Chloroflexi, an alternative carbon fixation pathway in anoxygenic photoautotrophs. Lastly, we recovered several abundant nitrogen fixation gene sequences associated with Roseiflexus, providing further evidence that genes involved in nitrogen fixation in Chloroflexi are more common than previously assumed. Together, our results add to the body of work on the distribution and functional potential of phototrophic bacteria in Yellowstone National Park hot springs and support the hypothesis that a combination of abiotic and biotic factors impact the distribution of phototrophic bacteria in hot springs. Future studies of isolates and metagenome assembled genomes (MAGs) from these data and others will further our understanding of the ecology and evolution of hot spring anoxygenic phototrophs. IMPORTANCE Photosynthetic bacteria in hot springs are of great importance to both microbial evolution and ecology. While a large body of work has focused on oxygenic photosynthesis in cyanobacteria in Mushroom and Octopus Springs in Yellowstone National Park, many questions remain regarding the metabolic potential and ecology of hot spring anoxygenic phototrophs. Anoxygenic phototrophs are metabolically and taxonomically diverse, and further investigations into their physiology will lead to a deeper understanding of microbial evolution and ecology of these taxa. Here, we have quantified the distribution of key genes involved in carbon and nitrogen metabolism in both oxygenic and anoxygenic phototrophs. Our results suggest that temperature >68ºC selects for distinct groups of cyanobacteria and that carbon fixation pathways associated with these taxa are likely subject to the same selective pressure. Additionally, our data suggest that phototrophic Chloroflexi genes and carbon fixation genes are largely influenced by local conditions as evidenced by our gene variant analysis. Lastly, we recovered several genes associated with potentially novel phototrophic Chloroflexi. Together, our results add to the body of work on hot springs in Yellowstone National Park and set the stage for future work on metagenome assembled genomes.

RevDate: 2022-05-16

Kawser AQMR, Foysal MJ, Chua EG, et al (2022)

Microbiome data reveal significant differences in the bacterial diversity in freshwater rohu (Labeo rohita) across the supply chain in Dhaka, Bangladesh.

Letters in applied microbiology [Epub ahead of print].

The present study aimed to characterize and compare the skin and gut microbial communities of rohu at various postharvest stages of consumption using quantitative real-time polymerase chain reaction and 16S rRNA-based amplicon sequencing. Real-time PCR amplification detected higher copy numbers for coliform bacteria- Escherichia coli, Salmonella enterica and Shigella spp. in the marketed fish, compared to fresh and frozen samples. The 16S rRNA data revealed higher alpha diversity measurements in the skin of fish from different retail markets of Dhaka city. Beta ordination revealed distinct clustering of bacterial OTUs for the skin and gut samples from three different groups. At the phylum level, Proteobacteria was most abundant in all groups except the Fusobacteria in the control fish gut. Although Aeromonas was found ubiquitous in all types of samples, diverse bacterial genera were identified in the marketed fish samples. Nonetheless, low species richness was observed for the frozen fish. Most of the differentially abundant bacteria in the skin samples of marketed fish are opportunistic human pathogens enriched at different stages of postharvest handling and processing. Therefore, considering the microbial contamination in the aquatic environment in Bangladesh, postharvest handling should be performed with proper methods and care to minimize bacterial transmission into fish.

RevDate: 2022-05-16

Beach NK, Myers KS, Donohue TJ, et al (2022)

Metagenomes from 25 Low-Abundance Microbes in a Partial Nitritation Anammox Microbiome.

Microbiology resource announcements [Epub ahead of print].

Microbial communities using anammox bacteria to remove nitrogen are increasingly important in wastewater treatment. We report on 25 metagenome-assembled genomes of low-abundance microbes from a partial nitritation anammox bioreactor system that have not been described previously. These data add to the body of information about this important wastewater treatment system.

RevDate: 2022-05-18

Goh CE, Bohn B, Marotz C, et al (2022)

Nitrite Generating and Depleting Capacity of the Oral Microbiome and Cardiometabolic Risk: Results from ORIGINS.

Journal of the American Heart Association, 11(10):e023038.

Background The enterosalivary nitrate-nitrite-nitric oxide (NO3-NO2-NO) pathway generates NO following oral microbiota-mediated production of salivary nitrite, potentially linking the oral microbiota to reduced cardiometabolic risk. Nitrite depletion by oral bacteria may also be important for determining the net nitrite available systemically. We examine if higher abundance of oral microbial genes favoring increased oral nitrite generation and decreased nitrite depletion is associated with a better cardiometabolic profile cross-sectionally. Methods and Results This study includes 764 adults (mean [SD] age 32 [9] years, 71% women) enrolled in ORIGINS (Oral Infections, Glucose Intolerance, and Insulin Resistance Study). Microbial DNA from subgingival dental plaques underwent 16S rRNA gene sequencing; PICRUSt2 was used to estimate functional gene profiles. To represent the different components and pathways of nitrogen metabolism in bacteria, predicted gene abundances were operationalized to create summary scores by (1) bacterial nitrogen metabolic pathway or (2) biochemical product (NO2, NO, or ammonia [NH3]) formed by the action of the bacterial reductases encoded. Finally, nitrite generation-to-depletion ratios of gene abundances were created from the above summary scores. A composite cardiometabolic Z score was created from cardiometabolic risk variables, with higher scores associated with worse cardiometabolic health. We performed multivariable linear regression analysis with cardiometabolic Z score as the outcome and the gene abundance summary scores and ratios as predictor variables, adjusting for sex, age, race, and ethnicity in the simple adjusted model. A 1 SD higher NO versus NH3 summary ratio was inversely associated with a -0.10 (false discovery rate q=0.003) lower composite cardiometabolic Z score in simple adjusted models. Higher NH3 summary score (suggestive of nitrite depletion) was associated with higher cardiometabolic risk, with a 0.06 (false discovery rate q=0.04) higher composite cardiometabolic Z score. Conclusions Increased net capacity for nitrite generation versus depletion by oral bacteria, assessed through a metagenome estimation approach, is associated with lower levels of cardiometabolic risk.

RevDate: 2022-05-16

Li F, Jiang L, Pan S, et al (2022)

Multi-omic Profiling Reveals that Intra-abdominal-Hypertension-Induced Intestinal Damage Can Be Prevented by Microbiome and Metabolic Modulations with 5-Hydroxyindoleacetic Acid as a Diagnostic Marker.

mSystems [Epub ahead of print].

Emerging evidence shows that modulation of the microbiome can suppress intra-abdominal hypertension (IAH)-induced intestinal barrier damage through the regulation of amino acid (AA) biosynthesis. Here, we investigated the protective effects of orally gavaged Lactobacillus acidophilus L-92 (L92) and a mixture of AA in rats with induced IAH. The results showed that both L92 and AA pretreatments effectively mitigated IAH-induced intestinal damage. Interestingly, L92 but not AA prevented metagenomic changes induced by IAH. Bacteroides fragilis, Bacteroides eggerthii, Bacteroides ovatus, Faecalibacterium prausnitzii, Prevotella, and extensively altered functional pathways were associated with L92-mediated host protection. Metabolomic profiling revealed that tryptophan metabolism was involved in both L92- and AA-mediated gut protection. The tryptophan metabolite 5-hydroxyindoleacetic acid (5-HIAA) is a sensitive biomarker for IAH in rats and patients with either gut-derived sepsis (n = 41) or all-source sepsis (n = 293). In conclusion, we show that microbiome and metabolic modulations can effectively prevent IAH-induced intestinal damage and that 5-HIAA is a potential metabolic marker for IAH and sepsis. IMPORTANCE Gut protection through modulation of the microbiome for critically ill patients has been gaining much attention recently. Intra-abdominal hypertension (IAH) is a prevailing clinical feature of acute gastrointestinal injuries in critically ill patients, characterized by nonspecific intestinal barrier damage. Prolonged IAH can induce or aggravate the development of sepsis and multiorgan dysfunctions. Therefore, the prevention of IAH-induced damage in rats through microbiome and metabolic interventions by commercially available L92 and AA treatments and the identification of 5-HIAA as an important marker for IAH/sepsis have important clinical implications for the treatment and early diagnosis of critically ill patients.

RevDate: 2022-05-17
CmpDate: 2022-05-17

Guo Y, Yang Y, Xu M, et al (2022)

Trends and Developments in the Detection of Pathogens in Central Nervous System Infections: A Bibliometric Study.

Frontiers in cellular and infection microbiology, 12:856845.

Introduction: Rapid, sensitive, and specific laboratory assays are critical for the diagnosis and management of central nervous system (CNS) infections. The purpose of this study is to explore the intellectual landscape of research investigating methods for the detection of pathogens in patients with CNS infections and to identify the development trends and research frontier in this field.

Methods: A bibliometric study is conducted by analyzing literature retrieved from the Web of Science (WoS) Core Collection Database for the years 2000 to 2021. CiteSpace software is used for bibliometric analysis and network visualization, including co-citation analysis of references, co-occurrence analysis of keywords, and cooperation network analysis of authors, institutions, and countries/regions.

Results: A total of 2,282 publications are eventually screened, with an upward trend in the number of publications per year. The majority of papers are attributed to the disciplines of MICROBIOLOGY, INFECTIOUS DISEASES, IMMUNOLOGY, NEUROSCIENCES & NEUROLOGY, and VIROLOGY. The co-citation analysis of references shows that recent research has focused on the largest cluster "metagenomic next-generation sequencing"; the results of the analysis of the highest-cited publications and the citation burst of publications reveal that there is a strong interest stimulated in metagenomic next-generation sequencing. The co-occurrence analysis of keywords indicates that "infection", "pathogen", "diagnosis", "gene", "virus", "polymerase chain reaction", "cerebrospinal fluid", "epidemiology", and "metagenomic next-generation sequencing" are the main research priorities in the field of pathogen detection for CNS infections, and the keyword with the highest strength of burst is "metagenomic next-generation sequencing". Collaborative network analysis reveals that the USA, the Centers for Disease Control and Prevention of USA, and XIN WANG and JENNIFER DIEN BARD are the most influential country, institution, and researchers, respectively.

Conclusions: Exploring more advanced laboratory assays to improve the diagnostic accuracy of pathogens is essential for CNS infection research. Metagenomic next-generation sequencing is emerging as a novel useful unbiased approach for diagnosing infectious diseases of the CNS.

RevDate: 2022-05-16

Ghosh A, Saha R, P Bhadury (2022)

Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem.

PeerJ, 10:e13169 pii:13169.

Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.

RevDate: 2022-05-16

Yu Y, Li L, Xu Y, et al (2022)

Metagenomics Reveals the Microbial Community Responsible for Producing Biogenic Amines During Mustard [Brassica juncea (L.)] Fermentation.

Frontiers in microbiology, 13:824644.

Biogenic amines (BAs) are considered potential hazards produced during fermented food processing, and the production of BAs is closely related to microbial metabolism. In this work, the changes of BA content were analyzed during mustard fermentation, and microbes and gene abundance responsible for producing BAs were revealed by metagenomic analyses. The results showed that cadaverine, putrescine, tyramine, and histamine were generated during mustard fermentation, which mainly accumulate in the first 6 days of fermentation. According to the metagenome sequencing, the predominant genus was Bacillus (64.78%), followed by Lactobacillus (11.67%), Weissella (8.88%), and Leuconostoc (1.71%) in the initial fermentation stage (second day), while Lactobacillus (76.03%) became the most dominant genus in the late stage. In addition, the gene abundance of BA production enzymes was the highest in the second day and decreased continuously as fermentation progressed. By tracking the source of the enzyme in the KEGG database, both Bacillus and Delftia closely correlated to the generation of putrescine. Besides, Bacillus also correlated to the generation of tyramine and spermidine, and Delftia also correlated to the generation of cadaverine and spermine. In the processes of fermentation, the pH of fermented mustard showed slower decrease compared with other similar fermented vegetables, which may allow Bacillus to grow at high levels before the pH <4. This study reveals the change of BA content and microbes involved in BA formation during mustard fermentation.

RevDate: 2022-05-16

Kharnaior P, JP Tamang (2022)

Metagenomic-Metabolomic Mining of Kinema, a Naturally Fermented Soybean Food of the Eastern Himalayas.

Frontiers in microbiology, 13:868383.

Kinema is a popular sticky fermented soybean food of the Eastern Himalayan regions of North East India, east Nepal, and south Bhutan. We hypothesized that some dominant bacteria in kinema may contribute to the formation of targeted and non-targeted metabolites for health benefits; hence, we studied the microbiome-metabolite mining of kinema. A total of 1,394,094,912 bp with an average of 464,698,304 ± 120,720,392 bp was generated from kinema metagenome, which resulted in the identification of 47 phyla, 331 families, 709 genera, and 1,560 species. Bacteria (97.78%) were the most abundant domain with the remaining domains of viruses, eukaryote, and archaea. Firmicutes (93.36%) was the most abundant phylum with 280 species of Bacillus, among which Bacillus subtilis was the most dominant species in kinema followed by B. glycinifermentans, B. cereus, B. licheniformis, B. thermoamylovorans, B. coagulans, B. circulans, B. paralicheniformis, and Brevibacillus borstelensis. Predictive metabolic pathways revealed the abundance of genes associated with metabolism (60.66%), resulting in 216 sub-pathways. A total of 361 metabolites were identified by metabolomic analysis (liquid chromatography-mass spectrophotometry, LC-MS). The presence of metabolites, such as chrysin, swainsonine, and 3-hydroxy-L-kynurenine (anticancer activity) and benzimidazole (antimicrobial, anticancer, and anti-HIV activities), and compounds with immunomodulatory effects in kinema supports its therapeutic potential. The correlation between the abundant species of Bacillus and primary and secondary metabolites was constructed with a bivariate result. This study proves that Bacillus spp. contribute to the formation of many targeted and untargeted metabolites in kinema for health-promoting benefits.

RevDate: 2022-05-17
CmpDate: 2022-05-17

Porto BN (2022)

Insights Into the Role of the Lung Virome During Respiratory Viral Infections.

Frontiers in immunology, 13:885341.

The virome constitutes the viral component of the microbiome and it consists of the genomes of all the viruses that inhabit a particular region of the human body, including those that cause acute, persistent or latent infection, and retroviral elements integrated to host chromosomes. The human virome is composed by eukaryotic viruses, bacteriophages and archaeal viruses. The understanding of the virome composition and role on human health has been delayed by the absence of specific tools and techniques to accurately characterize viruses. However, more recently, advanced methods for viral diagnostics, such as deep sequencing and metagenomics, have allowed a better understanding of the diverse viral species present in the human body. Previous studies have shown that the respiratory virome modulates the host immunity and that, since childhood, the human lung is populated by viruses for whom there is no disease association. Whether these viruses are potentially pathogenic and the reason for their persistence remain elusive. Increased respiratory viral load can cause exacerbation of chronic pulmonary diseases, including COPD, cystic fibrosis, and asthma. Moreover, the presence of resident viral populations may contribute to the pathogenesis of community-acquired respiratory virus infections. In this mini review, I will discuss the recent progress on our understanding of the human lung virome and summarize the up-to-date knowledge on the relationships among community-acquired respiratory viruses, the lung virome and the immune response to better understand disease pathophysiology and the factors that may lead to viral persistence.

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ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

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Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).

Timelines

ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.

Biographies

Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )