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Bibliography on: Metagenomics

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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 31 Jul 2021 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: 2021-07-30

Soares PET, Dantas MDA, Silva-Portela RCB, et al (2021)

Characterization of Penaeus vannamei mitogenome focusing on genetic diversity.

PloS one, 16(7):e0255291 pii:PONE-D-21-05194.

The diversity of the Penaeus vannamei mitochondrial genome has still been poorly characterized, there are no validated mitochondrial markers available for populational studies, and the heteroplasmy has not yet been investigated in this species. In this study, metagenomic reads extracted from the muscle of a single individual were used to assemble the mitochondrial genome (mtDNA). These data associated with mitochondrial genomes previously described allowed to evaluate the inter-individual variability and heteroplasmy. Comparison among 45 mtDNA control regions led to the detection of conserved and variable segments and the characterization of two hypervariable regions. The analysis of diversity revealed mostly low frequency polymorphisms, and heteroplasmy was found in practically all mitochondrial genes, with a high occurrence of indels. These results indicate that the design of mitochondrial markers for P. vannamei must be done with caution. The mapping of conserved and variable regions and the characterization of heteroplasmy presented here will contribute to increasing the efficiency of mitochondrial markers for population or individual studies.

RevDate: 2021-07-30

Kim NK, Lee SH, Yoon H, et al (2021)

Microbiome degrading linear alkylbenzene sulfonate in activated sludge.

Journal of hazardous materials, 418:126365 pii:S0304-3894(21)01329-7 [Epub ahead of print].

As the most widely used anionic surfactant, linear alkylbenzene sulfonate (LAS) requires biological alkane degradation when it is treated using an activated sludge (AS) process in a wastewater treatment plant because of its structural carboxylic unavailability. As consumption of LAS is gradually increasing, LAS loading into the WWTP is accordingly increasing. However, fewer studies have examined the involvement of the AS microbial community in the LAS degradation. In this study, metagenomic approaches were used to define microbiomes involved in LAS degradation in AS, with a particular focus on ω-hydroxylation. The abundance and diversity of alkane-degrading genes were investigated, and these genes were integrated with reconstructed metagenome-assembled genomes (MAGs). Additionally, the association of functional genes and MAGs with respect to LAS degradation was investigated. The results showed that alkB and cytochrome P450 genes were only shared within specific MAGs. Unique sets of genes with diverse abundances were detected in each sample. The MAGs with the alkB and cytochrome P450 genes were strongly associated with the other MAGs and involved in positive commensal interactions. The findings provided significant insights into how the AS microbiomes, which have continuously treated anionic surfactants for decades, potentially metabolize LAS and interact with commensal bacteria.

RevDate: 2021-07-30

Li J, Jia C, Lu Q, et al (2021)

Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures.

Journal of hazardous materials, 418:126384 pii:S0304-3894(21)01348-0 [Epub ahead of print].

Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.

RevDate: 2021-07-30

Karaolia P, Vasileiadis S, G Michael S, et al (2021)

Shotgun metagenomics assessment of the resistome, mobilome, pathogen dynamics and their ecological control modes in full-scale urban wastewater treatment plants.

Journal of hazardous materials, 418:126387 pii:S0304-3894(21)01351-0 [Epub ahead of print].

The conventional activated sludge (CAS) process has limited capacity to remove pathogenic microorganisms and antibiotic resistance genes (ARGs), compared to membrane bioreactors (MBRs). However, the full extent of pathogenic microbial fraction, resistome (antibiotic and biocide resistance genes, ARGs and BRGs) and mobilome (mobile genetic elements, MGE) of urban wastewater treatment plant (UWTP) influents and effluents remains unknown. Thus, the fate of putative pathogenic bacteria, ARGs and potential co-occurrence patterns with BRGs, MGEs and bacterial-predatory microorganisms was determined in two full-scale UWTPs, a MBR and a CAS system, using shotgun metagenomics. Both UWTPs significantly reduced the BOD5 (99.4-99.9%), COD (97.6-99.4%) and TSS (98.9-99.9%). MBR was more effective in reducing the abundance and diversity of pathogen-containing taxa, with 4 and 30 taxa enriched in MBR and CAS effluents, respectively. MBR treatment favored resistance genes associated with triclosan, whereas CAS effluents contained ARGs associated with antibiotics of clinical importance. Correlations between putative pathogenic bacteria, ARG/BRGs/MGEs and bacterial-predatory microorganisms suggested that: (i) opportunistic pathogens (Clostridia, Nocardia) may acquire ARGs against first-line treatments and (ii) bacteriophages may act as a biogenic mechanism of pathogen removal. These findings reinforce the MBR capacity to retain pathogenic components, hence reducing potential health risks associated with treated wastewater reuse.

RevDate: 2021-07-30

Arelli V, Mamindlapelli NK, Begum S, et al (2021)

Solid state anaerobic digestion of food waste and sewage sludge: Impact of mixing ratios and temperature on microbial diversity, reactor stability and methane yield.

The Science of the total environment, 793:148586 pii:S0048-9697(21)03658-5 [Epub ahead of print].

Food waste (FW) and sewage sludge (SS) were anaerobically co digested under solid state conditions (Total solids >15%) and observed that mixing ratio of 3:1 and 2:1 is optimum for mesophilic and thermophilic conditions respectively. The VS reduction and methane yield at optimized ratio was 76% and 0.35 L CH4/(g VS reduced) respectively at mesophilic temperature whereas it was 88% and 0.42 L CH4/(g VS reduced) at thermophilic temperature. The metagenomic analysis for these cases were done and high throughput DNA sequencing revealed that diversified bacterial groups that participate in the different metabolisms (hydrolysis, acidogenesis and acetogenesis) were mainly dominated by the phylum Firmicutes and Bacteriodetes. Genus Methanothrix is found to be dominant which is capable of generating methane by any methanogenic pathway among all the archaeal communities in the reactors followed by Methanolinea and Methanoculleus. However, it was understood through metagenomic studies that acetotrophic pathway is observed to be the major metabolic pathway in the reactors.

RevDate: 2021-07-30

Mora M, Wicaksono WA, Egamberdieva D, et al (2021)

Explorative assessment of coronavirus-like short sequences from host-associated and environmental metagenomes.

The Science of the total environment, 793:148494 pii:S0048-9697(21)03566-X [Epub ahead of print].

The ongoing COVID-19 pandemic has not only globally caused a high number of causalities, but is also an unprecedented challenge for scientists. False-positive virus detection tests not only aggravate the situation in the healthcare sector, but also provide ground for speculations. Previous studies have highlighted the importance of software choice and data interpretation in virome studies. We aimed to further expand theoretical and practical knowledge in bioinformatics-driven virome studies by focusing on short, virus-like DNA sequences in metagenomic data. Analyses of datasets obtained from different sample types (terrestrial, animal and human related samples) and origins showed that coronavirus-like sequences have existed in host-associated and environmental samples before the current COVID-19 pandemic. In the analyzed datasets, various Betacoronavirus-like sequences were detected that also included SARS-CoV-2 matches. Deepening analyses indicated that the detected sequences are not of viral origin and thus should not be considered in virome profiling approaches. Our study confirms the importance of parameter selection, especially in terms of read length, for reliable virome profiling. Natural environments are an important source of coronavirus-like nucleotide sequences that should be taken into account when virome datasets are analyzed and interpreted. We therefore suggest that processing parameters are carefully selected for SARS-CoV-2 profiling in host related as well as environmental samples in order to avoid incorrect identifications.

RevDate: 2021-07-30

Fu X, Ou Z, Zhang M, et al (2021)

Classroom microbiome, functional pathways and sick-building syndrome (SBS) in urban and rural schools - Potential roles of indoor microbial amino acids and vitamin metabolites.

The Science of the total environment, 795:148879 pii:S0048-9697(21)03951-6 [Epub ahead of print].

Sick building symptoms (SBS) are defined as non-specific symptoms related to indoor exposures, including mucosal symptoms in eye, nose, throat, and skin, and general symptoms as headache and tiredness. Indoor microbial composition is associated with SBS symptoms, but the impact of microbial functional genes and potential metabolic products has not been characterized. We conducted a shotgun microbial metagenomic sequencing for vacuum dust collected in urban and rural schools in Shanxi province, China. SBS symptoms in students were surveyed, and microbial taxa and functional pathways related to the symptoms were identified using a multi-level linear regression model. SBS symptoms were common in students, and the prevalence of ocular and throat symptoms, headache, and tiredness was higher in urban than in rural areas (p < 0.05). A significant higher microbial α-diversity was found in rural areas than in urban areas (Chao1, p = 0.001; ACE, p = 0.002). Also, significant variation in microbial taxonomic and functional composition (β-diversity) was observed between urban and rural areas (p < 0.005). Five potential risk Actinobacteria species were associated with SBS symptoms (p < 0.01); students in the classrooms with a higher abundance of an unclassified Geodermatophilaceae, Geodermatophilus, Fridmanniella luteola, Microlunatus phosphovorus and Mycetocola reported more nasal and throat symptoms and tiredness. Students with a higher abundance of an unclassified flavobacteriaceae reported fewer throat symptoms and tiredness. The abundance of microbial metabolic pathways related to the synthesis of B vitamins (biotin and folate), gamma-aminobutyric acid (GABA), short-chain fatty acids (SCFAs), and peptidoglycan and were protectively (negatively) associated with SBS symptoms (FDR < 0.05). The result is consistent with human microbiota studies, which reported that these microbial products are extensively involved in immunological processes and anti-inflammatory effects. This is the first study to report the functional potential of the indoor microbiome and the occurrence of SBS, providing new insights into the potential etiologic mechanisms in chronic inflammatory diseases.

RevDate: 2021-07-30

Yao GJ, Ren JQ, Zhou F, et al (2021)

Micro-nano aeration is a promising alternative for achieving high-rate partial nitrification.

The Science of the total environment, 795:148899 pii:S0048-9697(21)03971-1 [Epub ahead of print].

Biological nitrogen removal is the most prevalent wastewater nitrogen removal process but nitrification limits the rate of the whole process mainly due to the low efficiency of oxygen transfer. In this study, clean-water oxygenation tests, batch tests, long-term operational tests and metagenomic analyses were applied to assess the effects of micro-nano aeration on nitrification. The oxygen transfer coefficient (KLa), oxygen transfer rate (OTR) and oxygen transfer efficiency (OTE) were determined to be 0.56 min-1, 0.36 kg·m-3·h-1 and 71.43%, respectively during micro-nano-bubble aeration. Impressively, these values were 15 times greater than those of conventional aeration. The results of batch tests and long-term operation experiments found that the ammonia removal rate of micro-nano aeration was 3.2-fold that of conventional aeration. The energy cost for micro-nano aeration was calculated to be 3694.5 mg NH4+-N/kW·h, a 50% energy saving in comparison to conventional aeration. In addition, the nitrite accumulation ratio in the Micro-nano (MN) reactor was 1.5 that of the Conventional (CV) reactor. Metagenomic analysis showed that after long-term operation in micro-nano aeration, the abundances of genes encoding ammonia monooxygenase (amoA) and hydroxylamine oxidoreductase (hao) was more than 8-fold and 4-fold of those in conventional aeration, respectively. The abundance of the gene encoding nitrite oxidoreductase (nxrA) was similar in both reactors. Read taxonomy revealed that abundance of AOB-Nitrosomonas increased significantly when using micro-nano aeration, while abundance of NOB-Nitrospira abundance was similar in both reactors. The results of this study indicated that the micro-nano aeration process will increase the ammonia oxidation performance by enhancing oxygen transfer but was also shown to be beneficial for enhancing partial nitrification by specific enrichment of ammonia oxidizing bacteria. This latter result demonstrates the potential benefits of the micro-nano aeration process as an alternative approach to establishing high-rate partial nitrification.

RevDate: 2021-07-30

Hausherr D, Niederdorfer R, Morgenroth E, et al (2021)

Robustness of mainstream anammox activity at bench and pilot scale.

The Science of the total environment, 796:148920 pii:S0048-9697(21)03992-9 [Epub ahead of print].

New technologies and processes, such as mainstream anammox, aim to reduce energy requirements of wastewater treatment and improve effluent quality. However, in municipal wastewater (MWW) anammox system are often unstable due to process control disturbance, influent variability, or unwanted nitrite oxidizing bacteria (NOB). This study examines the anammox system by focusing on anammox activity and its robustness in a mainstream environment. An 8 m3 pilot-scale sequencing batch reactor (SBR) receiving pretreated MWW (with external nitrite addition) was seeded with pre-colonized carriers. Within six months at 12-20 °C an anammox activity of 200 gN·m-3·d-1 was achieved. After the startup an anammox activity of 260 ± 83 gN·m-3·d-1 was maintained over 450 days. The robustness of the anammox activity was analyzed through three disturbance experiments. Anammox biofilm on carriers were exposed to dissolved oxygen (DO = 1.6 mg·L-1, intermittent aeration), organic loading rate (OLR, C/N increased from 2:1 to 5:1) and temperature disturbances (20 °C to 12 °C) in triplicate 12 L bench scale reactors. The anammox activity and microbial community was monitored during these disturbances. The DO and OLR disturbance experiments were replicated at pilot scale to investigate upscaling effects. Bench and pilot scale anammox activity were unaffected by the DO disturbance. Similarly, an increase in OLR did not deteriorate the bench and pilot scale anammox activity, if nitrate was available. When, at bench scale, the reactor temperature was reduced from 20 °C to 12 °C overnight, anammox activity decreased significantly, this was not the case for the slow seasonal temperature changes (12-25 °C) at pilot scale where no strong temperature dependency was detected in winter. Metagenomic analysis revealed a broad range of Brocadiaceae species with no single dominant anammox species. Anammox thrive under mainstream conditions and can withstand typical process disruptions.

RevDate: 2021-07-30

Marongiu L, Landry JJM, Rausch T, et al (2021)

Metagenomic analysis of primary colorectal carcinomas and their metastases identifies potential microbial risk factors.

Molecular oncology [Epub ahead of print].

The paucity of microbiome studies at intestinal tissues has contributed to a yet limited understanding of potential viral and bacterial co-factors of colorectal cancer (CRC) carcinogenesis or progression. We analyzed whole-genome sequences of CRC primary tumours, their corresponding metastases and matched normal tissue for sequences of viral, phage and bacterial species. Bacteriome analysis showed Fusobacterium nucleatum, Streptococcus sanguinis, F. Hwasookii, Anaerococcus mediterraneensis and further species enriched in primary CRCs. The primary CRC of one patient was enriched for F. alocis, S. anginosus, Parvimonas micra and Gemella sp. 948. Enrichment of Escherichia coli strains IAI1, SE11, K-12 and M8 was observed in metastases together with coliphages enterobacteria phage φ80 and Escherichia phage VT2φ_272. Virome analysis showed that phages were the most preponderant viral species (46%), the main families being Myoviridae, Siphoviridae and Podoviridae. Primary CRCs were enriched for bacteriophages, showing five phages (Enterobacteria, Bacillus, Proteus, Streptococcus phages) together with their pathogenic hosts in contrast to normal tissues. The most frequently detected, and Blast-confirmed, viruses included human endogenous retrovirus K113, human herpesviruses 7 and 6B, Megavirus chilensis, cytomegalovirus (CMV) and Epstein-Barr virus (EBV), with one patient showing EBV enrichment in primary tumour and metastases. EBV was PCR-validated in 80 pairs of CRC primary tumour and their corresponding normal tissues; in 21 of these pairs (26.3%), it was detectable in primary tumours only. The number of viral species was increased and bacterial species decreased in CRCs compared with normal tissues,and we could discriminate primary CRCs from metastases and normal tissues by applying the Hutcheson t-test on the Shannon indices based on viral and bacterial species. Taken together, our results descriptively support hypotheses on microorganisms as potential (co-)risk factors of CRC, and extend putative suggestions on critical microbiome species in CRC metastasis.

RevDate: 2021-07-30

d'Humières C, Salmona M, Dellière S, et al (2021)

The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives.

Drugs [Epub ahead of print].

Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples to obtain clinically relevant information such as the identification of microorganisms and their susceptibility to antimicrobials. Over the last decades, sequencing and bioinformatic solutions supporting CMg have much evolved and an increasing number of case reports and series covering various infectious diseases have been published. Metagenomics is a new approach to infectious disease diagnosis that is currently being developed and is certainly one of the most promising for the coming years. However, most CMg studies are retrospective, and few address the potential impact CMg could have on patient management, including initiation, adaptation, or cessation of antimicrobials. In this narrative review, we have discussed the potential role of CMg in bacteriology, virology, mycology, and parasitology. Several reports and case-series confirm that CMg is an innovative tool with which one can (i) identify more microorganisms than with conventional methods in a single test, (ii) obtain results within hours, and (iii) tailor the antimicrobial regimen of patients. However, the cost-efficiency of CMg and its real impact on patient management are still to be determined.

RevDate: 2021-07-30

Nishikawa H, Fukunishi S, Asai A, et al (2021)

Dysbiosis and liver diseases (Review).

International journal of molecular medicine, 48(3):.

Dysbiosis, a qualitative and quantitative aberrancy of gut microbiota, has attracted marked attention. At present, advances in molecular biological techniques have made it possible to analyze gut microbiota at the DNA and RNA levels without culturing, and methods such as 16S ribosomal RNA targeting analysis and metagenomic analysis using next‑generation sequencers have been developed. The relationship between gut microbiota and various diseases has been extensively examined. Gut microbiota are essential for the immune system, energy intake and fat storage, and humans use them to build complex immune regulatory mechanisms and to obtain energy from food. The liver is the first organ to be nourished by the portal blood flow of intestinal origin, and liver diseases can be strongly influenced by various factors of intestinal origin, such as intestinal bacteria, bacterial components, and intestinal bacterial metabolites. Rigorous research has revealed that the composition of the gut microbiota is altered and the diversity of bacteria is reduced in liver diseases. Significance of various factors transported to the liver by portal vein blood flow from the intestine has been extensively investigated. Gut microbiota in liver disease can be associated with disease progression regardless of disease etiology and even with carcinogenesis. The relationship between gut microbiota and liver diseases (hepatitis virus‑related diseases, autoimmune liver diseases, alcoholic liver disease, non‑alcoholic fatty liver disease, non‑alcoholic steatohepatitis, liver cirrhosis and hepatocellular carcinoma) and the treatments of dysbiosis (antibiotics, prebiotics, probiotics and fecal microbiota transplantation) in liver disease are outlined based on the current evidence.

RevDate: 2021-07-30

Wang S, Yong H, XD He (2021)

Multi-omics: Opportunities for research on mechanism of type 2 diabetes mellitus.

World journal of diabetes, 12(7):1070-1080.

Type 2 diabetes mellitus (T2DM) is a burdensome global disease. In-depth understanding of its mechanism will help to optimize diagnosis and treatment, which reduces the burden. Multi-omics research has unparalleled advantages in contributing to the overall understanding of the mechanism of this chronic metabolic disease. In the past two decades, the study of multi-omics on T2DM-related intestinal flora perturbation and plasma dyslipidemia has shown tremendous potential and is expected to achieve major breakthroughs. The regulation of intestinal flora in diabetic patients has been confirmed by multiple studies. The use of metagenomics, 16S RNA sequencing, and metabolomics has comprehensively identified the overall changes in the intestinal flora and the metabolic disturbances that could directly or indirectly participate in the intestinal flora-host interactions. Lipidomics combined with other "omics" has characterized lipid metabolism disorders in T2DM. The combined application and cross-validation of multi-omics can screen for dysregulation in T2DM, which will provide immense opportunities to understand the mechanisms behind T2DM.

RevDate: 2021-07-30

Scavizzi F, Bassi C, Lupini L, et al (2021)

A comprehensive approach for microbiota and health monitoring in mouse colonies using metagenomic shotgun sequencing.

Animal microbiome, 3(1):53.

BACKGROUND: Health surveillance of murine colonies employed for scientific purposes aim at detecting unwanted infection that can affect the well-being of animals and personnel, and potentially undermine scientific results. In this study, we investigated the use of a next-generation sequencing (NGS) metagenomic approach for monitoring the microbiota composition and uncovering the possible presence of pathogens in mice housed in specific pathogen-free (SPF) or conventional (non-SPF) facilities.

RESULTS: Analysis of metagenomic NGS assay through public and free algorithms and databases allowed to precisely assess the composition of mouse gut microbiome and quantify the contribution of the different microorganisms at the species level. Sequence analysis allowed the uncovering of pathogens or the presence of imbalances in the microbiota composition. In several cases, fecal pellets taken from conventional facilities were found to carry gene sequences from bacterial pathogens (Helicobacter hepaticus, Helicobacter typhlonius, Chlamydia muridarum, Streptococcus pyogenes, Rodentibacter pneumotropicus, Citrobacter rodentium, Staphylococcus aureus), intestinal protozoa (Entamoeba muris, Tritrichomonas muris, Spironucleus muris) nematoda (Aspiculuris tetraptera, Syphacia obvelata), eukaryotic parasites (Myocoptes musculinus) and RNA virus (Norwalk virus). Thus, the use of NGS metagenomics can reduce the number of tests required for the detection of pathogens and avoid the use of sentinel mice.

CONCLUSIONS: In summary, in comparison with standard approaches, which require multiple types of test, NGS assay can detect bacteria, fungi, DNA and RNA viruses, and eukaryotic parasites from fecal pellets in a single test. Considering the need to protect animal well-being and to improve the success and reproducibility of preclinical studies, this work provides the proof-of-concept that the use of NGS metagenomics for health monitoring of laboratory mice is a feasible and dependable approach, that is able to broaden the current concept of health monitoring of laboratory mice from "pathogen surveillance" to a more inclusive "microbiota surveillance".

RevDate: 2021-07-30

Sakamoto T, JM Ortega (2021)

Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree.

BMC bioinformatics, 22(1):388.

BACKGROUND: NCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions deposited on INSDC are organized in its hierarchical structure. Despite the extensive use and application of this data source, an alternative representation of data as a table would facilitate the use of information for processing bioinformatics data. To do so, since some taxonomic-ranks are missing in some lineages, an algorithm might propose provisional names for all taxonomic-ranks.

RESULTS: To address this issue, we developed an algorithm that takes the tree structure from NCBI Taxonomy and generates a hierarchically complete taxonomic table, maintaining its compatibility with the original tree. The procedures performed by the algorithm consist of attempting to assign a taxonomic-rank to an existing clade or "no rank" node when possible, using its name as part of the created taxonomic-rank name (e.g. Ord_Ornithischia) or interpolating parent nodes when needed (e.g. Cla_of_Ornithischia), both examples given for the dinosaur Brachylophosaurus lineage. The new hierarchical structure was named Taxallnomy because it contains names for all taxonomic-ranks, and it contains 41 hierarchical levels corresponding to the 41 taxonomic-ranks currently found in the NCBI Taxonomy database. From Taxallnomy, users can obtain the complete taxonomic lineage with 41 nodes of all taxa available in the NCBI Taxonomy database, without any hazard to the original tree information. In this work, we demonstrate its applicability by embedding taxonomic information of a specified rank into a phylogenetic tree and by producing metagenomics profiles.

CONCLUSION: Taxallnomy applies to any bioinformatics analyses that depend on the information from NCBI Taxonomy. Taxallnomy is updated periodically but with a distributed PERL script users can generate it locally using NCBI Taxonomy as input. All Taxallnomy resources are available at http://bioinfo.icb.ufmg.br/taxallnomy .

RevDate: 2021-07-30
CmpDate: 2021-07-30

Sibai M, Altuntaş E, Yıldırım B, et al (2020)

Microbiome and Longevity: High Abundance of Longevity-Linked Muribaculaceae in the Gut of the Long-Living Rodent Spalax leucodon.

Omics : a journal of integrative biology, 24(10):592-601.

With a world population living longer as well as marked disparities in life expectancy, understanding the determinants of longevity is one of the priority research agendas in 21st century life sciences. To this end, the blind mole-rat (Spalax leucodon), a subterranean mammalian, has emerged as an exceptional model organism due to its astonishing features such as remarkable longevity, hypoxia and hypercapnia tolerance, and cancer resistance. The microbiome has been found to be a vital parameter for cellular physiology and it is safe to assume that it has an impact on life expectancy. Although the unique characteristics of Spalax make it an ideal experimental model for longevity research, there is limited knowledge of the bacterial composition of Spalax microbiome, which limits its in-depth utilization. In this study, using 16S rRNA amplicon sequencing, we report the gut and skin bacterial structure of Spalax for the first time. The diversity between fecal and skin samples was manifested in the distant clustering, as revealed by beta diversity analysis. Importantly, the longevity-linked Muribaculaceae bacterial family was found to be the dominating bacterial taxa in Spalax fecal samples. These new findings contribute toward further development of Spalax as a model for longevity research and potential linkages between microbiome composition and longevity.

RevDate: 2021-07-29

Yadav A, Yadav P, Kumar Singh A, et al (2021)

Decolourisation of textile dye by laccase: Process evaluation and assessment of its degradation bioproducts.

Bioresource technology, 340:125591 pii:S0960-8524(21)00932-9 [Epub ahead of print].

Biodegradation of environmentally hazardous synthetic dyes by enzymes has been achieved the highest interest in recent years. In this work, we optimized Remazol Brilliant Blue R (RBBR) dye biodegradation by Arthrographis kalrae derived laccase via the Box-Behnken design (BBD) approach of the surface response methodology (RSM). Optimization of dye decolourisation by one variable at a time (OVAT) approach resulted in optimal dye decolourisation at laccase dose (2 IU mL-1), pH (7.0), temperature (35 °C), incubation time (240 min), and initial dye concentration (100 mg L-1). The optimized process through BBD enhanced dye decolourisation (97.18%). Fourier Transform Infrared Spectroscopy and UV-Visible Spectrophotometry have proven biodegradation. In addition, in comparison to untreated samples, the laccase-treated dye sample showed relatively less phyto- and cytotoxic effect on Allium cepa L. Extra Precision Glide docking exhibited the binding affinity score of -5.355 kcal mol-1, between laccase-RBBR complex.

RevDate: 2021-07-29

Singh G, Tiwari A, Gupta A, et al (2021)

Bioformulation development via valorizing silica-rich spent mushroom substrate with Trichoderma asperellum for plant nutrient and disease management.

Journal of environmental management, 297:113278 pii:S0301-4797(21)01340-2 [Epub ahead of print].

The present investigation was performed to valorize paddy straw (PS) based silica (Si) rich Spent Mushroom Substrate (SMS) of Pleurotus ostreatus for Plant Nutrient and Disease Management in wilt (caused by F. oxysporum f. sp. lycopersici) susceptible tomato plant F1 Hybrid King 180. Raw PS and SMS generated by P. ostreatus cultivated on PS only, and PS amended with 5% soybean cake (SC) were bio-fortified with Trichoderma asperellum (TA). SMS (PS+ 5% SC) was found supporting the growth of T. asperellum to an extent of 12.37 × 1013 conidia/g substrate. GC-MS analysis of SMS detected several bioactive metabolites like Palmitic acid, Oleic acid, Methyl linoleate, Stigmasterol, etc., known for plant health management. Bioformulations were developed employing Press Mud (PM) and Talcum Powder (TP) as carrier materials. Among the different bioformulations tested in pots study; SMS (PS+ 5% SC) SiTAPM, collectively named as TF-I, provided improved levels of morpho-biochemical and nutritional parameters, i.e., Plant Biomass (2.27 folds), Root Volume (1.75 folds), Chlorophyll (2.66 folds), Carotenoids (2.42 folds), Number of Fruits (1.76 folds), Fruit Biomass (2.02 folds), Total Soluble Sugars (2.32 folds), Total Soluble Proteins (1.70 folds), and nutraceutical parameters as Lycopene (1.42 folds), β-carotene (2.65 folds) and Ascorbic Acid (1.54 folds), along with significant (p < 0.05) reduction in the Disease Severity Index (84.34%-21.23%), over the pathogen affected plant taken as control. The fruits and leaves garnered under TF-I displayed Total Polyphenol Content (TPC) of 74.5 and 126.9 mg g-1 gallic acid, respectively, with 83.73% DPPH and 72.25% FRAP activity, indicating the elicitation of antioxidant properties in tomato fruits. EDS analyses showed 21.53% Si in SMS, and plant mapping investigation indicated a substantial accumulation of Si, which is well conceded to promote growth, disease resistance, and antioxidant parameters. The study also endorsed the use of PM over TP, as TF-I recorded an acceptable conidial count (2.22 × 108 cfu/g) towards the end of six months storage period over other bioformulations. Overall, the study envisages the development and application of innovative methodology (TF-I), offering an eco-friendly alternative for producing quality crops and a sustainable solution to waste management, thus delivering a holistic contribution towards the circular economy.

RevDate: 2021-07-29

Wang M, Sun Y, Zeng Z, et al (2021)

Metagenomics of wastewater phageome identifies an extensively cored antibiotic resistome in a swine feedlot water treatment environment.

Ecotoxicology and environmental safety, 222:112552 pii:S0147-6513(21)00664-3 [Epub ahead of print].

Huge number of antibiotic resistance genes (ARGs) have been widely detected in phage genomes from anthropogenic environment or animal farms, whereas little is known about the dynamic changes of phage contribution to resistance under a feedlot wastewater treatment facility (WTF) pressure. Here, a metagenomics method was used to characterize the sewage phageome and identifies the antibiotic resistome. The results showed that the phage families of Siphoviridae, Myoviridae, and Podoviridae were always the most dominant. Analysis of ARGs carried by bacterial and phages showed that MLS and tetracycline resistance genes always had the highest abundances and the other ARG types also have a fixed hierarchy, showing that there is no significant change in overall ARGs abundance distribution. However, an extensively cored antibiotic resistome were specifically identified in aerobic environment. ARGs encoding ribosomal protection proteins, especially for the ARG subtypes lsaE, tet44, tetM, tetP, macB, MdlB and rpoB2, were more inclined to be selected by phages, suggesting that a more refined mechanism, such as specialized transduction and lateral transduction, was probably involved. In all, these results suggest that monitoring of dynamic changes of phage contribution to resistance should be given more attention and ARGs-carrying phage management should focus on using technologies for controlling cored ARGs rather than only the overall distribution of ARGs in phages.

RevDate: 2021-07-29

Liu S, Wang P, Wang C, et al (2021)

Anthropogenic disturbances on antibiotic resistome along the Yarlung Tsangpo River on the Tibetan Plateau: Ecological dissemination mechanisms of antibiotic resistance genes to bacterial pathogens.

Water research, 202:117447 pii:S0043-1354(21)00645-X [Epub ahead of print].

Human activities can accelerate the antibiotic resistome prevalence and pose threats to ecological safety and public health globally. However, antibiotic resistance gene (ARG) mobility and dissemination into bacterial pathogens under anthropogenic disturbances are still poorly understood. Here, we used a metagenomic approach to profile the biogeography of ARGs and pathogenic antibiotic resistant bacteria (PARB) under anthropogenic disturbances along the Yarlung Tsangpo River. Results showed the ARGs was dominated by bacA gene along the Yarlung Tsangpo River on the Tibetan Plateau. The ARG composition was differently impacted by rapid urbanization and dam construction, which urbanization could promote ARGs resistant to sulfonamide and tetracycline, whereas dam construction could elevate the resistance to chloramphenicol and aminoglycoside. Land use pattern was identified as a critical factor influencing ARG composition under anthropogenic disturbances, as it could directly reflect the land degradation level and indicate the inputs of ARG-selective chemicals of different human activities. Moreover, despite of the lack of variation in ARG relative abundance, PARB were highly promoted by anthropogenic activities, indicating increasing ARG dissemination to pathogen. We found that human-impacted environments harbored high proportion of mobile genetic elements (MGEs), and the MGE carrying ARGs also increased under anthropogenic disturbances in the pathogenic hosts, which confirmed that anthropogenic activities could promote ARG horizontal gene transfer. Furthermore, anthropogenic activities could influence PARB assembly processes. Basically, stochastic processes dominated PARB assembly along the river, and with increasing level of anthropogenic activities, these processes shifted from undominated stochastic processes to dispersal limitation. In summary, this study provides useful strategies in watershed resistome management and reduction of ARG dissemination to pathogens, which should consider the mode and intensity of human activity and its potential influence on horizontal gene transfer and assembly processes.

RevDate: 2021-07-29

Campos PE, Groot Crego C, Boyer K, et al (2021)

First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence.

PLoS pathogens, 17(7):e1009714 pii:PPATHOGENS-D-20-02385.

Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.

RevDate: 2021-07-29

Blaise D, Velmourougane K, Santosh S, et al (2021)

Intercrop mulch affects soil biology and microbial diversity in rainfed transgenic Bt cotton hybrids.

The Science of the total environment, 794:148787 pii:S0048-9697(21)03859-6 [Epub ahead of print].

Growing live mulch between the wide-row spaced transgenic Bt cotton hybrids is a low-cost option to control weeds compared to the use of plastic mulch. However, nothing is known about their effects on soil biology. Therefore, soil samples were collected from a long-term field study (2014-15 to 2018-19) to investigate the soil biological activities as well as the microbial diversity (soil metagenomic analysis). In general, mulching enhanced soil biological activity and influenced the microbial diversity in Bt-cotton. Mulch of sunnhemp (Crotalaria juncea L.), desmodium (Desmodium triflorum L.), sorghum (Sorghum bicolor L.) and plastic sheet recorded significantly higher soil biological activities such as, basal respiration, microbial biomass carbon, and soil enzymes than the other mulch treatments. Aromatic crops (bitter cumin (Centratherum anthelminticum (L.) Kuntze), carom (Trachyspermum ammi (L.) Sprague ex Turrill), coriander (Coriandrum sativum L.), fennel (Foeniculum vulgare Mill.), and fenugreek (Trigonella foenum-graecum L.) had a significant adverse effect on soil biological activity compared to the farmers' practice (no mulch or intercrop). The rarefaction curves as a measure of alpha diversity indicated higher species richness in plastic and newspaper sheet mulch treatments compared to the intercrop mulch. The soil metagenome data indicated Proteobacteria (28%-36%), Actinobacteria (10%-35%), and Acidobacteria (10%-26%) were highly abundant phyla in the mulch treatments. The phyla, Chloroflexi (4%-5%), Gemmatimonadetes (2%-6%), Planctomycetes (2%-4%), and Bacteroidetes (2%-3%) were recorded at lower frequencies in all mulch treatments. The sunnhemp and newspaper mulch treatments recorded low frequency (0.06%-0.07%) of the fungal phyla, Ascomycota. Compared to the bare soil, mulching positively improves soil biological activity. Furthermore, our study identifies some crops that could be grown as an intercrop with a viewpoint to improve soil biology and provide an alternative to the expensive plastic mulch.

RevDate: 2021-07-29

Murray B, Dailey M, Ertekin E, et al (2021)

Draft Metagenomes of Endolithic Cyanobacteria and Cohabitants from Hyper-Arid Deserts.

Microbiology resource announcements, 10(30):e0020621.

Cyanobacteria are essential to microbial communities inhabiting translucent rocks in hyper-arid deserts. Metagenomic studies revealed unique adaptations of these cyanobacteria, but validation of the corresponding metabolic pathways remained challenging without access to isolates. Here, we present high-quality metagenome-assembled genomes for cyanobacteria, and their heterotrophic companions, isolated from endolithic substrates.

RevDate: 2021-07-29

Sun Y, Snow D, Walia H, et al (2021)

Transmission Routes of the Microbiome and Resistome from Manure to Soil and Lettuce.

Environmental science & technology [Epub ahead of print].

The land application of animal manure can introduce manure microbiome and resistome to croplands where food crops are grown. The objective of this study was to characterize the microbiome and resistome on and in the leaves of lettuce grown in manured soil and identify the main transmission routes of microbes and antibiotic resistance genes (ARGs) from soil to the episphere and endosphere of lettuce. Shotgun metagenomic results show that manure application significantly altered the composition of the microbiome and resistome of surface soil. SourceTracker analyses indicate that manure and original soil were the main source of the microbiome and resistome of the surface soil and rhizosphere soil, respectively. Manure application altered the microbiome and resistome in the episphere of lettuce (ADONIS p < 0.05), and surface soil accounted for ∼81% of the microbes and ∼62% of the ARGs in episphere. Manure application had limited impacts on the microbiome and resistome in the endosphere (ADONIS p > 0.05). Our results show that manure-borne microbes and ARGs reached the episphere primarily through surface soil and some epiphytic microbes and ARGs further entered the endosphere. Our findings can inform the development of pre- and postharvest practices to minimize the transmission of manure-borne resistome from food crops to consumers.

RevDate: 2021-07-29

Ramchandar N, Burns J, Coufal NG, et al (2021)

Use of Metagenomic Next-Generation Sequencing to Identify Pathogens in Pediatric Osteoarticular Infections.

Open forum infectious diseases, 8(7):ofab346 pii:ofab346.

Background: Osteoarticular infections (OAIs) are frequently encountered in children. Treatment may be guided by isolation of a pathogen; however, operative cultures are often negative. Metagenomic next-generation sequencing (mNGS) allows for broad and sensitive pathogen detection that is culture-independent. We sought to evaluate the diagnostic utility of mNGS in comparison to culture and usual care testing to detect pathogens in acute osteomyelitis and/or septic arthritis in children.

Methods: This was a single-site study to evaluate the use of mNGS in comparison to culture to detect pathogens in acute pediatric osteomyelitis and/or septic arthritis. Subjects admitted to a tertiary children's hospital with suspected OAI were eligible for enrollment. We excluded subjects with bone or joint surgery within 30 days of admission or with chronic osteomyelitis. Operative samples were obtained at the surgeon's discretion per standard care (fluid or tissue) and based on imaging and operative findings. We compared mNGS to culture and usual care testing (culture and polymerase chain reaction [PCR]) from the same site.

Results: We recruited 42 subjects over the enrollment period. mNGS of the operative samples identified a pathogen in 26 subjects compared to 19 subjects in whom culture identified a pathogen. In 4 subjects, mNGS identified a pathogen where combined usual care testing (culture and PCR) was negative. Positive predictive agreement and negative predictive agreement both were 93.0% for mNGS.

Conclusions: In this single-site prospective study of pediatric OAI, we demonstrated the diagnostic utility of mNGS testing in comparison to culture and usual care (culture and PCR) from operative specimens.

RevDate: 2021-07-29

Yang S, He Y, Chen X, et al (2021)

Viral Metagenomics Reveals Diverse Viruses in the Feces Samples of Raccoon Dogs.

Frontiers in veterinary science, 8:693564.

Raccoon dogs as an ancient species of Canidae are the host of many viruses, including rabies virus, canine distemper virus, severe acute respiratory syndrome coronavirus, and so on. With the development of raccoon dog breeding in recent years, some viruses which infected poultry or pigs were also detected from raccoon dogs. At present, the fecal virome of raccoon dogs has been rarely studied. Using an unbiased viral metagenomic approach, we investigated the fecal virome in raccoon dogs collected from one farm of Jilin Province, China. Many DNA or RNA viruses identified in those fecal samples were mainly from seven families, including Circoviridae, Smacoviridae, Genomoviridae, Parvoviridae, Picornaviridae, Astroviridae, and Hepeviridae. This study increased our understanding of the fecal virome in raccoon dog and provided valuable information for the monitoring, prevention, and treatment of viral diseases of these animals.

RevDate: 2021-07-29

Ye Y, Yang N, Zhou J, et al (2021)

Case Report: Metagenomic Next-Generation Sequencing in Diagnosis of Disseminated Tuberculosis of an Immunocompetent Patient.

Frontiers in medicine, 8:687984.

Disseminated tuberculosis (TB) is a rare disease and mainly occurs in immunodeficient patients. It is marked by hematogenous or lymphatic dissemination of Mycobacterium tuberculosis, causing tuberculous infection involving any organ system. Here, we report a case of disseminated TB involving lung, liver, spine, mediastinum, and prostate in an immunocompetent man. The present patient found a hepatic mass without any symptom during health examination. In the next 2 years, further examinations revealed multiple lesions in the lung, mediastinum, spine, and prostate. Imaging examinations, such as contrast-enhanced abdominal CT, F-18 FDG-PET/CT, and radionuclide bone scan, suggested the diagnosis of malignancy or metastatic tumor. Furthermore, histopathological results of the biopsies of the hepatic mass, mediastinal mass, and prostatic mass demonstrated granulomatous inflammation. Therefore, metagenomic next-generation sequencing (mNGS) was utilized to confirm the diagnosis. Mycobacterium tuberculosis complex was simultaneously detected in the spinal surgical resection specimens and bronchoalveolar lavage fluid (BALF), indicating the diagnosis of disseminated TB. mNGS is an emerging molecular diagnostic technology, and its application in disseminated TB has been rarely reported. We highlight that disseminated TB should be considered even in an immunocompetent patient, and mNGS can be performed when the diagnosis is difficult.

RevDate: 2021-07-29

Zhou J, Theroux SM, Bueno de Mesquita CP, et al (2021)

Microbial drivers of methane emissions from unrestored industrial salt ponds.

The ISME journal [Epub ahead of print].

Wetlands are important carbon (C) sinks, yet many have been destroyed and converted to other uses over the past few centuries, including industrial salt making. A renewed focus on wetland ecosystem services (e.g., flood control, and habitat) has resulted in numerous restoration efforts whose effect on microbial communities is largely unexplored. We investigated the impact of restoration on microbial community composition, metabolic functional potential, and methane flux by analyzing sediment cores from two unrestored former industrial salt ponds, a restored former industrial salt pond, and a reference wetland. We observed elevated methane emissions from unrestored salt ponds compared to the restored and reference wetlands, which was positively correlated with salinity and sulfate across all samples. 16S rRNA gene amplicon and shotgun metagenomic data revealed that the restored salt pond harbored communities more phylogenetically and functionally similar to the reference wetland than to unrestored ponds. Archaeal methanogenesis genes were positively correlated with methane flux, as were genes encoding enzymes for bacterial methylphosphonate degradation, suggesting methane is generated both from bacterial methylphosphonate degradation and archaeal methanogenesis in these sites. These observations demonstrate that restoration effectively converted industrial salt pond microbial communities back to compositions more similar to reference wetlands and lowered salinities, sulfate concentrations, and methane emissions.

RevDate: 2021-07-29

Nathani NM, Dave KJ, Vatsa PP, et al (2021)

309 metagenome assembled microbial genomes from deep sediment samples in the Gulfs of Kathiawar Peninsula.

Scientific data, 8(1):194.

Prokaryoplankton genomes from the deep marine sediments are less explored compared to shallow shore sediments. The Gulfs of Kathiawar peninsula experience varied currents and inputs from different on-shore activities. Any perturbations would directly influence the microbiome and their normal homeostasis. Advancements in reconstructing genomes from metagenomes allows us to understand the role of individual unculturable microbes in ecological niches like the Gulf sediments. Here, we report 309 bacterial and archaeal genomes assembled from metagenomics data of deep sediments from sites in the Gulf of Khambhat and Gulf of Kutch as well as a sample from the Arabian Sea. Phylogenomics classified them into 5 archaeal and 18 bacterial phyla. The genomes will facilitate understanding of the physiology, adaptation and impact of on-shore anthropogenic activities on the deep sediment microbes.

RevDate: 2021-07-29

Motamedi E, Kavousi K, Sadeghian Motahar SF, et al (2021)

Efficient removal of various textile dyes from wastewater by novel thermo-halotolerant laccase.

Bioresource technology, 337:125468.

A novel thermostable/halotolerant metagenome-derived laccase (PersiLac2) from tannery wastewater was purified to remove textile dyes in this study. The enzyme was highly active over a wide temperature and pH range and maintained 73.35% of its initial activity after 30 days, at 50 °C. The effect of various metal and organic-solvent tolerance on PersiLac2 showed, retaining greater than 53% activity at 800 mM of metal ions, 52.12% activity at 6 M NaCl, and greater than 44.09% activity at 20% organic solvents. PersiLac2 manifested effective removal of eight different textile dyes from azo, anthraquinone, and triphenylmethane families. It decolorized 500 mg/L of Alizarin yellow, Carmine, Congo red and Bromothymol blue with 99.74-55.85% efficiency after 15 min, at 50 °C, without mediator. This enzyme could practically remove dyes from a real textile effluent and it displayed significant detoxification in rice seed germination tests. In conclusion, PersiLac2 could be useful in future for decolorization/detoxification of wastewater.

RevDate: 2021-07-28

Manni M, Berkeley MR, Seppey M, et al (2021)

BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes.

Molecular biology and evolution pii:6329644 [Epub ahead of print].

Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying datasets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate dataset for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly-introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets.

RevDate: 2021-07-28

Jacot D, Pillonel T, Greub G, et al (2021)

Assessment of SARS-CoV-2 genome sequencing: quality criteria and low frequency variants.

Journal of clinical microbiology [Epub ahead of print].

Although many laboratories worldwide have developed their sequencing capacities in response to the need for SARS-CoV-2 genome-based surveillance of variants, only few reported some quality criteria to ensure sequence quality before lineage assignment and submission to public databases. Hence, we aimed here to provide simple quality control criteria for SARS-CoV-2 sequencing to prevent erroneous interpretation of low quality or contaminated data. We retrospectively investigated 647 SARS-CoV-2 genomes obtained over ten tiled amplicons sequencing runs. We extracted 26 potentially relevant metrics covering the entire workflow from sample selection to bioinformatics analysis. Based on data distribution, critical values were established for eleven selected metrics to prompt further quality investigations for problematic samples, in particular those with a low viral RNA quantity. Low frequency variants (<70% of supporting reads) can result from PCR amplification errors, sample cross contaminations or presence of distinct SARS-CoV2 genomes in the sample sequenced. The number and the prevalence of low frequency variants can be used as a robust quality criterion to identify possible sequencing errors or contaminations. Overall, we propose eleven metrics with fixed cutoff values as a simple tool to evaluate the quality of SARS-CoV-2 genomes, among which cycle thresholds, mean depth, proportion of genome covered at least 10x and the number of low frequency variants combined with mutation prevalence data.

RevDate: 2021-07-28

Cezar RM, Vezzani FM, Kaschuk G, et al (2021)

Crop rotation reduces the frequency of anaerobic soil bacteria in Red Latosol of Brazil.

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] [Epub ahead of print].

Crop diversity affects the processes of soil physical structuring and most likely provokes changes in the frequencies of soil microbial communities. The study was conducted for soil prokaryotic diversity sequencing 16S rDNA genes from a 25-year no-tillage experiment comprised of two crop systems: crop succession (Triticum aestivum-Glycine max) and rotation (Vicia sativa-Zea mays-Avena sativa-Glycine max-Triticum aestivum-Glycine max). The hypothesis was that a crop system with higher crop diversification (rotation) would affect the frequencies of prokaryotic taxa against a less diverse crop system (succession) altering the major soil functions guided by bacterial diversity. Soils in both crop systems were dominated by Proteobacteria (31%), Acidobacteria (23%), Actinobacteria (10%), and Gemmatimonadetes (7.2%), among other common copiotrophic soil bacteria. Crop systems did not affect the richness and diversity indexes of soil bacteria and soil archaea. However, the crop rotation system reduced only the frequencies of anaerobic metabolism bacteria Chloroacidobacteria, Holophagae, Spirochaetes, Euryarchaeota, and Crenarchaeota. It can be concluded that crop succession, a system that is poorer in root diversity over time, may have conditioned the soil to lower oxygen diffusion and built up ecological niches that suitable for anaerobic bacteria tolerating lower levels of oxygen. On the other hand, it appeared that crop rotation has restructured the soil over the years while enabling copiotrophic aerobic bacteria to dominate the soil ecosystem. The changes prompted by crop succession have implications for efficient soil organic matter decomposition, reduced greenhouse gas emissions, higher root activity, and overall soil productivity, which compromise to agriculture sustainability.

RevDate: 2021-07-28

Tarallo S, Ferrero G, De Filippis F, et al (2021)

Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals.

Gut pii:gutjnl-2021-325168 [Epub ahead of print].

OBJECTIVES: MicroRNA (miRNA) profiles have been evaluated in several biospecimens in relation to common diseases for which diet may have a considerable impact. We aimed at characterising how specific diets are associated with the miRNome in stool of vegans, vegetarians and omnivores and how this is reflected in the gut microbial composition, as this is still poorly explored.

DESIGN: We performed small RNA and shotgun metagenomic sequencing in faecal samples and dietary recording from 120 healthy volunteers, equally distributed for the different diets and matched for sex and age.

RESULTS: We found 49 miRNAs differentially expressed among vegans, vegetarians and omnivores (adj. p <0.05) and confirmed trends of expression levels of such miRNAs in vegans and vegetarians compared with an independent cohort of 45 omnivores. Two miRNAs related to lipid metabolism, miR-636 and miR-4739, were inversely correlated to the non-omnivorous diet duration, independently of subject age. Seventeen miRNAs correlated (|rho|>0.22, adj. p <0.05) with the estimated intake of nutrients, particularly animal proteins, phosphorus and, interestingly, lipids. In omnivores, higher Prevotella and Roseburia and lower Bacteroides abundances than in vegans and vegetarians were observed. Lipid metabolism-related miR-425-3p and miR-638 expression levels were associated with increased abundances of microbial species, such as Roseburia sp. CAG 182 and Akkermansia muciniphila, specific of different diets. An integrated analysis identified 25 miRNAs, 25 taxa and 7 dietary nutrients that clearly discriminated (area under the receiver operating characteristic curve=0.89) the three diets.

CONCLUSION: Stool miRNA profiles are associated with specific diets and support the role of lipids as a driver of epigenetic changes and host-microbial molecular interactions in the gut.

RevDate: 2021-07-29
CmpDate: 2021-07-29

Xie J, Z Zhu (2021)

A case report of pyogenic liver abscess caused by hypervirulent Klebsiella pneumoniae diagnosed by metagenomic next-generation sequencing.

The Journal of international medical research, 49(7):3000605211032793.

A 56-year-old woman with a history of diabetes mellitus presented with high fever but no abdominal pain. An abdominal computed tomography scan showed a large liver abscess. Hypervirulent, string test-positive, rmpA/ampA2-, and iutA-positive Klebsiella pneumoniae was rapidly identified from drainage fluid of the liver abscess using metagenomic next-generation sequencing (mNGS). After intravenous antibiotic therapy and drainage of the abscess, the patient's condition resolved. This case report highlights the value of mNGS in rapidly and accurately identifying a pathogenic microorganism, which helps reduce the incidence of antimicrobial resistance and enables the targeted use of antibiotics.

RevDate: 2021-07-28
CmpDate: 2021-07-28

Molik DC, Tomlinson D, Davitt S, et al (2021)

Combining natural language processing and metabarcoding to reveal pathogen-environment associations.

PLoS neglected tropical diseases, 15(4):e0008755.

Cryptococcus neoformans is responsible for life-threatening infections that primarily affect immunocompromised individuals and has an estimated worldwide burden of 220,000 new cases each year-with 180,000 resulting deaths-mostly in sub-Saharan Africa. Surprisingly, little is known about the ecological niches occupied by C. neoformans in nature. To expand our understanding of the distribution and ecological associations of this pathogen we implement a Natural Language Processing approach to better describe the niche of C. neoformans. We use a Latent Dirichlet Allocation model to de novo topic model sets of metagenetic research articles written about varied subjects which either explicitly mention, inadvertently find, or fail to find C. neoformans. These articles are all linked to NCBI Sequence Read Archive datasets of 18S ribosomal RNA and/or Internal Transcribed Spacer gene-regions. The number of topics was determined based on the model coherence score, and articles were assigned to the created topics via a Machine Learning approach with a Random Forest algorithm. Our analysis provides support for a previously suggested linkage between C. neoformans and soils associated with decomposing wood. Our approach, using a search of single-locus metagenetic data, gathering papers connected to the datasets, de novo determination of topics, the number of topics, and assignment of articles to the topics, illustrates how such an analysis pipeline can harness large-scale datasets that are published/available but not necessarily fully analyzed, or whose metadata is not harmonized with other studies. Our approach can be applied to a variety of systems to assert potential evidence of environmental associations.

RevDate: 2021-07-29
CmpDate: 2021-07-29

Pavlova YS, Paez-Espino D, Morozov AY, et al (2021)

Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling.

PLoS computational biology, 17(3):e1008841.

Understanding CRISPR-Cas systems-the adaptive defence mechanism that about half of bacterial species and most of archaea use to neutralise viral attacks-is important for explaining the biodiversity observed in the microbial world as well as for editing animal and plant genomes effectively. The CRISPR-Cas system learns from previous viral infections and integrates small pieces from phage genomes called spacers into the microbial genome. The resulting library of spacers collected in CRISPR arrays is then compared with the DNA of potential invaders. One of the most intriguing and least well understood questions about CRISPR-Cas systems is the distribution of spacers across the microbial population. Here, using empirical data, we show that the global distribution of spacer numbers in CRISPR arrays across multiple biomes worldwide typically exhibits scale-invariant power law behaviour, and the standard deviation is greater than the sample mean. We develop a mathematical model of spacer loss and acquisition dynamics which fits observed data from almost four thousand metagenomes well. In analogy to the classical 'rich-get-richer' mechanism of power law emergence, the rate of spacer acquisition is proportional to the CRISPR array size, which allows a small proportion of CRISPRs within the population to possess a significant number of spacers. Our study provides an alternative explanation for the rarity of all-resistant super microbes in nature and why proliferation of phages can be highly successful despite the effectiveness of CRISPR-Cas systems.

RevDate: 2021-07-29
CmpDate: 2021-07-29

An J, McDowell A, Kim YK, et al (2021)

Extracellular vesicle-derived microbiome obtained from exhaled breath condensate in patients with asthma.

Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology, 126(6):729-731.

RevDate: 2021-07-28
CmpDate: 2021-07-28

Psonis N, Antoniou A, Karameta E, et al (2021)

The wall lizards of the Balkan peninsula: Tackling questions at the interface of phylogenomics and population genomics.

Molecular phylogenetics and evolution, 159:107121.

Wall lizards of the genus Podarcis (Sauria, Lacertidae) are the predominant reptile group in southern Europe, including 24 recognized species. Mitochondrial DNA data have shown that, with the exception of P. muralis, the Podarcis species distributed in the Balkan peninsula form a species group that is further sub-divided into two subgroups: the one of "P. tauricus" consisting of P. tauricus, P. milensis, P. gaigeae, and P. melisellensis, and the other of "P. erhardii" comprising P. erhardii, P. levendis, P. cretensis, and P. peloponnesiacus. In an attempt to explore the Balkan Podarcis phylogenomic relationships, assess the levels of genetic structure and to re-evaluate the number of extant species, we employed phylogenomic and admixture approaches on ddRADseq (double digested Restriction site Associated DNA sequencing) genomic data. With this efficient Next Generation Sequencing approach, we were able to obtain a large number of genomic loci randomly distributed throughout the genome and use them to resolve the previously obscure phylogenetic relationships among the different Podarcis species distributed in the Balkans. The obtained phylogenomic relationships support the monophyly of both aforementioned subgroups and revealed several divergent lineages within each subgroup, stressing the need for taxonomic re-evaluation of Podarcis' species in Balkans. The phylogenomic trees and the species delimitation analyses confirmed all recently recognized species (P. levendis, P. cretensis, and P. ionicus) and showed the presence of at least two more species, one in P. erhardii and the other in P. peloponnesiacus.

RevDate: 2021-07-28
CmpDate: 2021-07-28

Li Y, Burridge CP, Lv Y, et al (2021)

Morphometric and population genomic evidence for species divergence in the Chimarrichthys fish complex of the Tibetan Plateau.

Molecular phylogenetics and evolution, 159:107117.

The uplift of the Tibetan Plateau altered the environmental conditions of the local area substantially. Here, we conducted a comprehensive investigation based on morphometrics, population genomics, and climatic factors to evaluate phenotypic and genome-level variations in a radiation of Chimarrichthys catfish endemic to the Plateau. Discriminant function analysis showed phenotypic differences of Chimarrichthys between rivers with respect to elevation. Genetic structure analysis based on 6606 single nucleotide polymorphisms (SNPs) deduced genetic differences between rivers, and species delimitation indicated that the Chimarrichthys fish complex could be divided into three species. Restriction site-associated DNA tags were mapped to the gene sets of Glyptosternon maculatum, and matches were searched against databases for Gene Ontology annotation. Genomic regions exhibiting marked differences among localities represented a range of biological functions, including growth (gdf11), bone development (bmp8a), cellular response to light stimulus (opn3), regulation of the rhodopsin-mediated signalling pathway (grk1), immune response (rag1 and ung), reproductive process (antxr2), and regulation of intracellular iron levels (ireb2). The tag44126, where gene gdf11 is located, was identified as an outlier exhibiting divergence between rivers with altitude differences, and the SNP is thymine (T) in Dadu and Yalong River (~2700 m), but guanine (G) in Jinsha and Qingyi rivers (~2200 and ~ 684 m), suggesting a possible effect of altitude on its differentiation.

RevDate: 2021-07-29
CmpDate: 2021-07-29

Ghemrawi M, Torres AR, Duncan G, et al (2021)

The genital microbiome and its potential for detecting sexual assault.

Forensic science international. Genetics, 51:102432.

Since its inception, the Human Microbiome Project (HMP) has provided key discoveries that can be applied to forensics, in addition to those of obvious medical value. Whether for postmortem interval estimation, geolocation, or human identification, there are many applications of the microbiome as an investigative lead for forensic casework. The human skin microbiome has shown great potential for use in studies of transfer and human identification, however there has been little focus on the genital microbiome, in particular penile skin which differs from other body sites. Our preliminary data on both the penile and vaginal microbiome demonstrates potential value in cases of sexual assault. In this study we describe genital microbial signatures based on the analysis of five male and five female genital samples and compare these results to those from longitudinal studies. Selected taxa, e.g., Gardnerella, Lactobacilli, Finegoldia, Peptoniphilus, and Anaerococci, are shown to be candidate constituents of the genital microbiome that merit investigation for use in sexual assault casework.

RevDate: 2021-07-27

Kamau E, Maliksi E, Kwan N, et al (2021)

Catabacter hongkongensis bacteremia identified by direct metagenomic sequencing of positive blood culture fluid, first case report in the US.

Catabacter hongkongensis, an increasingly recognized bacteria in clinical samples, was identified by direct metagenomic sequencing of positive blood culture fluid from a 55-year-old patient with colonic perforation. The bacteremia was cleared by both antibiotic treatment and surgical intervention. This is the first case report of C. hongkongensis infection in the US.

RevDate: 2021-07-28

Palevich N, PH Maclean (2021)

Sequencing and Reconstructing Helminth Mitochondrial Genomes Directly from Genomic Next-Generation Sequencing Data.

Methods in molecular biology (Clifton, N.J.), 2369:27-40.

We present a detailed method for extraction of high-molecular weight genomic DNA suitable for numerous DNA sequencing applications, and a straightforward in silico approach for reconstructing novel mitochondrial (mt) genomes directly from total genomic DNA extracts derived from next-generation sequencing (NGS) data sets. The in silico post-sequencing pipeline described is fast, accurate, and highly efficient, with modest memory requirements that can be performed using a standard desktop computer. The approach is particularly effective for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information currently available and overcomes many of the limitations of traditional strategies. The described methodologies are also applicable for metagenomics sequencing from mixed or pooled samples containing multiple species and subsequent specific assembly of specific mitochondrial genomes.

RevDate: 2021-07-27

Hao Z, Tao K, Wu K, et al (2021)

Alterations of gut microbiome and metabolite profiles in choledocholithiasis concurrent with cholangitis.

Hepatology international [Epub ahead of print].

BACKGROUND AND AIMS: Gut microbiota and their metabolic products might play important roles in regulating the pathogenesis of choledocholithiasis concurrent with cholangitis (CC). The aim of this study was to explore the characteristic gut dysbiosis, metabolite profiles and the possible roles in patients with CC.

METHODS: A case-control study was carried out to analyze the alterations in the intestinal microbiota and their metabolites in patients with CC (n = 25) compared with healthy controls (HCs) (n = 25) by metagenomic sequencing to define the gut microbiota community and liquid chromatography/mass spectrometry (LC/MS) analysis to characterize the metabolite profiles.

RESULTS: Significantly reduced Shannon diversity index (p = 0.043) and differential overall fecal microbiota community in CCs were observed. Twelve dominant altered species were identified and analyzed (LDA score > 3.0, p < 0.05) (Q value < 0.05), including unclassified_f_Enterobacteriaceae, Escherichia_coli, Roseburia_faecis and Eubacterium rectale. Moreover, the levels of KEGG pathways related to biofilm formation of Escherichia coli, lipopolysaccharide (LPS) biosynthesis, and the metabolism of propanoate and glutathione in CCs were significantly altered. Finally, 47 markedly changed metabolites (VIP > 1.0 and p < 0.05), including low level of kynurenic acid (KYNA) and high concentration of N-palmitoylsphingosine involving tryptophan metabolism and sphingolipid signaling pathways, were identified to validate aberrant metabolic patterns in CCs, and multiple correlated metabolic modules involving bile inflammation were altered in CCs.

CONCLUSION: Our study provides novel insights into compositional and functional alterations in the gut microbiome and metabolite profiles in CC and the underlying mechanisms between gut microbiota and bile inflammation.

RevDate: 2021-07-28

Gacesa R, Vich Vila A, Collij V, et al (2021)

A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease.

Gut microbes, 13(1):1943288.

Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) show a large overlap in clinical presentation, which presents diagnostic challenges. As a consequence, invasive and burdensome endoscopies are often used to distinguish between IBD and IBS. Here, we aimed to develop a noninvasive fecal test that can distinguish between IBD and IBS and reduce the number of endoscopies.We used shotgun metagenomic sequencing to analyze the composition and function of gut microbiota of 169 IBS patients, 447 IBD patients and 1044 population controls and measured fecal Calprotectin (FCal), human beta defensin 2 (HBD2), and chromogranin A (CgA) in these samples. These measurements were used to construct training sets (75% of data) for logistic regression and machine learning models to differentiate IBS from IBD and inactive from active IBD. The results were replicated on test sets (remaining 25% of the data) and microbiome data obtained using 16S sequencing.Fecal HBD2 showed high sensitivity and specificity for differentiating between IBD and IBS (sensitivity = 0.89, specificity = 0.76), while the inclusion of microbiome data with biomarkers (HBD2 and FCal) showed a potential for improvement in predictive power (optimal sensitivity = 0.87, specificity = 0.93). Shotgun sequencing-based models produced comparable results using 16S-sequencing data. HBD2 and FCal were found to have predictive power for IBD disease activity (AUC ≈ 0.7).HBD2 is a novel biomarker for IBD in patients with gastro-intestinal complaints, especially when used in combination with FCal and potentially in combination with gut microbiome data.

RevDate: 2021-07-27

Li YX, Rao YZ, Qi YL, et al (2021)

Deciphering Symbiotic Interactions of "Candidatus Aenigmarchaeota" with Inferred Horizontal Gene Transfers and Co-occurrence Networks.

mSystems [Epub ahead of print].

"Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota") represents one of the earliest proposed evolutionary branches within the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, their ecological roles and potential host-symbiont interactions are still poorly understood. Here, eight metagenome-assembled genomes (MAGs) were reconstructed from hot spring ecosystems, and further in-depth comparative and evolutionary genomic analyses were conducted on these MAGs and other genomes downloaded from public databases. Although with limited metabolic capacities, we reported that "Ca. Aenigmarchaeota" in thermal environments harbor more genes related to carbohydrate metabolism than "Ca. Aenigmarchaeota" in nonthermal environments. Evolutionary analyses suggested that members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota contribute substantially to the niche expansion of "Ca. Aenigmarchaeota" via horizontal gene transfer (HGT), especially genes related to virus defense and stress responses. Based on co-occurrence network results and recent genetic exchanges among community members, we conjectured that "Ca. Aenigmarchaeota" may be symbionts associated with one MAG affiliated with the genus Pyrobaculum, though host specificity might be wide and variable across different "Ca. Aenigmarchaeota" organisms. This study provides significant insight into possible DPANN-host interactions and ecological roles of "Ca. Aenigmarchaeota." IMPORTANCE Recent advances in sequencing technology promoted the blowout discovery of super tiny microbes in the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) superphylum. However, the unculturable properties of the majority of microbes impeded our investigation of their behavior and symbiotic lifestyle in the corresponding community. By integrating horizontal gene transfer (HGT) detection and co-occurrence network analysis on "Candidatus Aenigmarchaeota" ("Ca. Aenigmarchaeota"), we made one of the first attempts to infer their putative interaction partners and further decipher the potential functional and genetic interactions between the symbionts. We revealed that HGTs contributed by members from the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota (TACK) superphylum and Euryarchaeota conferred "Ca. Aenigmarchaeota" with the ability to survive under different environmental stresses, such as virus infection, high temperature, and oxidative stress. This study demonstrates that the interaction partners might be inferable by applying informatics analyses on metagenomic sequencing data.

RevDate: 2021-07-27

Caddey B, Orsel K, Naushad S, et al (2021)

Identification and Quantification of Bovine Digital Dermatitis-Associated Microbiota across Lesion Stages in Feedlot Beef Cattle.

mSystems [Epub ahead of print].

Bovine digital dermatitis (DD) is a skin disorder that is a significant cause of infectious lameness in cattle around the world. However, very little is known about the etiopathogenesis of the disease and the microbiota associated with DD in beef cattle. In this study, we provide a comprehensive characterization of DD and healthy skin microbiota of feedlot beef cattle. We also developed and validated a novel multiplex quantitative PCR (qPCR) assay to quantify the distribution of DD-associated bacterial species across DD lesion stages. We determined the DD-associated microbiota with deep amplicon sequencing of the V3-V4 hypervariable region of the 16S rRNA gene, followed by the application of novel and existing qPCR assays to quantify species distributions of Treponema, Porphyromonas, Fusobacterium, and Bacteroides across lesion stages. Deep amplicon sequencing revealed that Treponema, Mycoplasma, Porphyromonas, and Fusobacterium were associated with DD lesions. Culturing of DD biopsy specimens identified Porphyromonas levii, Bacteroides pyogenes, and two Fusobacterium spp. within DD lesions. Using species-specific qPCR on DD lesion DNA, we identified P. levii in 100% of active lesion stages. Early-stage lesions were particularly associated with Treponema medium, T. phagedenis, and P. levii. This study suggests a core DD microbial group consisting of species of Treponema, Fusobacterium, Porphyromonas, and Bacteroides, which may be closely tied with the etiopathogenesis of DD. Further characterizations of these species and Mycoplasma spp. are necessary to understand the microbial factors involved in DD pathogenesis, which will help elucidate DD etiology and facilitate more targeted and effective mitigation and treatment strategies. IMPORTANCE Previous work, primarily in dairy cattle, has identified various taxa associated with digital dermatitis (DD) lesions. However, there is a significant gap in our knowledge of DD microbiology in beef cattle. In addition, characterization of bacteria at the species level in DD lesions is limited. In this study, we provide a framework for the accurate and reproducible quantification of major DD-associated bacterial species from DNA samples. Our findings support DD as a polymicrobial infection, and we identified a variety of bacterial species spanning multiple genera that are consistently associated with DD lesions. The DD-associated microbiota identified in this study may be capable of inducing the formation and progression of DD lesions and thus should be primary targets in future DD pathogenesis studies.

RevDate: 2021-07-27

Valença IN, Bezerra RDS, de Oliveira LCO, et al (2021)

Deep viral metagenomics in patients with haemophilia receiving plasma-derived coagulation factor concentrates.

RevDate: 2021-07-27

Wippel K, Tao K, Niu Y, et al (2021)

Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota.

Nature microbiology [Epub ahead of print].

Roots of different plant species are colonized by bacterial communities, that are distinct even when hosts share the same habitat. It remains unclear to what extent the host actively selects these communities and whether commensals are adapted to a specific plant species. To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics. We analysed taxonomically paired synthetic communities from L. japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations. Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host. Our findings show that host preference in commensal bacteria from diverse taxonomic groups is associated with their invasiveness into standing root-associated communities.

RevDate: 2021-07-27

Ottoni C, Borić D, Cheronet O, et al (2021)

Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus.

Proceedings of the National Academy of Sciences of the United States of America, 118(32):.

Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

RevDate: 2021-07-27

Wan Y, Zuo T, Xu Z, et al (2021)

Underdevelopment of the gut microbiota and bacteria species as non-invasive markers of prediction in children with autism spectrum disorder.

Gut pii:gutjnl-2020-324015 [Epub ahead of print].

OBJECTIVE: The gut microbiota has been suggested to play a role in autism spectrum disorder (ASD). We postulate that children with ASD harbour an altered developmental profile of the gut microbiota distinct from that of typically developing (TD) children. Here, we aimed to characterise compositional and functional alterations in gut microbiome in association with age in children with ASD and to identify novel faecal bacterial markers for predicting ASD.

DESIGN: We performed deep metagenomic sequencing in faecal samples of 146 Chinese children (72 ASD and 74 TD children). We compared gut microbial composition and functions between children with ASD and TD children. Candidate bacteria markers were identified and validated by metagenomic analysis. Gut microbiota development in relation to chronological age was assessed using random forest model.

RESULTS: ASD and chronological age had the most significant and largest impacts on children's faecal microbiome while diet showed no correlation. Children with ASD had significant alterations in faecal microbiome composition compared with TD children characterised by increased bacterial richness (p=0.021) and altered microbiome composition (p<0.05). Five bacterial species were identified to distinguish gut microbes in ASD and TD children, with areas under the receiver operating curve (AUC) of 82.6% and 76.2% in the discovery cohort and validation cohort, respectively. Multiple neurotransmitter biosynthesis related pathways in the gut microbiome were depleted in children with ASD compared with TD children (p<0.05). Developing dynamics of growth-associated gut bacteria (age-discriminatory species) seen in TD children were lost in children with ASD across the early-life age spectrum.

CONCLUSIONS: Gut microbiome in Chinese children with ASD was altered in composition, ecological network and functionality compared with TD children. We identified novel bacterial markers for prediction of ASD and demonstrated persistent underdevelopment of the gut microbiota in children with ASD which lagged behind their respective age-matched peers.

RevDate: 2021-07-27

Quince C, Nurk S, Raguideau S, et al (2021)

STRONG: metagenomics strain resolution on assembly graphs.

Genome biology, 22(1):214.

We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.

RevDate: 2021-07-23

Checcucci A, Luise D, Modesto M, et al (2021)

Assessment of Biolog EcoplateTM method for functional metabolic diversity of aerotolerant pig fecal microbiota.

Applied microbiology and biotechnology [Epub ahead of print].

In the last decades, gut microbiota and its role in mammal host development and health have been increasingly investigated. Metabolites produced by gut microbiota can affect intestinal homeostasis and immune system maturity and activation, and in turn, they can influence the health and growth performance of livestock. Therefore, a better understanding of the functional metabolic capability of the gut microbiota would be appreciated by the scientific community. In this study, the BiologTM Ecoplates technology was applied for studying the metabolic potential of the aerotolerant microbial community of pig fecal samples, evaluating the interference of different storage conditions and cell concentrations. The length of time for which a fecal sample maintained detectable and unchanged microbial metabolic activity was also investigated. Two assays aimed to evaluate differences in the metabolic activities between fresh and snap-frozen fecal samples at different dilutions and at different lengths of times of preservation at -80°C were carried out. The biodiversity and the predicted functionality of the entire bacterial community through a targeted metagenomic approach were also explored. The results highlighted that snap freezing of fecal samples preserved the metabolic activity of the microbial community when compared to fresh feces. Sample storage at -80 °C did not significantly affect the metabolic activity of the microbial community, which was stable for 150 days. Furthermore, the highest metabolic activity was detected with 1:2 to 1:5 dilutions of the stock suspension. BiologTM Ecoplates technology is a rapid and useful method to explore microbial communities' metabolism in animal fecal samples contributing to investigate host animal physiology. KEY POINTS: • Freezing of samples can preserve the functional activity of the aerotolerant microbial community for 150 days. • The concentration of microbial cells strongly influences metabolic activity detection. • Sequencing coupled with the BiologTM Ecoplates could be a strategy to evaluate the metabolic potential of the microbiota of the fecal sample.

RevDate: 2021-07-23

Szabó G, Schulz F, Manzano-Marín A, et al (2021)

Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles.

The ISME journal [Epub ahead of print].

Adelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelges tardus species complex containing betaproteobacterial ("Candidatus Vallotia tarda") and gammaproteobacterial ("Candidatus Profftia tarda") symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other's role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

RevDate: 2021-07-23

Andrade BGN, Goris T, Afli H, et al (2021)

Putative mobilized colistin resistance genes in the human gut microbiome.

BMC microbiology, 21(1):220.

BACKGROUND: The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes.

RESULTS: A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings.

CONCLUSION: This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.

RevDate: 2021-07-26

Shekhawat SS, Kulshreshtha NM, Vivekanand V, et al (2021)

Impact of combined chlorine and UV technology on the bacterial diversity, antibiotic resistance genes and disinfection by-products in treated sewage.

Bioresource technology, 339:125615 pii:S0960-8524(21)00956-1 [Epub ahead of print].

This paper explores the effect of hybrid chlorine and UV disinfection treatment against their individual usage on microbial community, functional genes, antibiotic resistant genes (ARGs) and disinfection by-products (DBPs) formation. The disinfectant doses of 2.5 mg L-1 chlorine and 41 mJ cm-2 UV were selected based on the coliform counts to be attained in treated sewage. The highest bacterial diversity was observed in control (secondary treated) sample followed by UV, chlorine and hybrid disinfection. The highest elimination of bacterial species (296) was achieved in hybrid treatment, which was far better than the standalone treatments. The disinfection with all the disinfectants used resulted in increased abundance of ARGs. Motility genes were found to be enriched in hybrid disinfected samples. DBP concentrations were within the stipulated norms for all the disinfectant treatments used. Hybrid disinfection was observed to be more effective in alleviating the risks associated with the reuse of treated sewage.

RevDate: 2021-07-26

Polo C, García-Seco T, Hernández M, et al (2021)

Evaluation of PCR assays for Campylobacter fetus detection and discrimination between C. fetus subspecies in bovine preputial wash samples.

Theriogenology, 172:300-306 pii:S0093-691X(21)00225-9 [Epub ahead of print].

Campylobacter fetus is a zoonotic pathogen found in cattle, in which it is one of the main causes of infectious infertility. Most diagnostic laboratories use PCR as quick easy tool for C. fetus identification. However, there is no standardized PCR assay for C. fetus detection and subspecies differentiation, hindering the comparison of results. In this study, we evaluated selected PCR assays targeting the 16S rRNA, gyrB, cpn60, cstA, cdtB and nahE genes for C. fetus identification and ISCfe1, sapB2, parA and virB11 for subspecies differentiation. Analytical sensitivity and specificity were assessed for each PCR assay, and the assays were then tested on 289 bull preputial samples that had also been analysed by 16S rRNA barcode metagenomics. In total, 41 C. fetus-positive samples were included. The P12 PCR assay targeting the gyrB gene performed best, detecting the pathogen in 95.1% of positive samples. For the discrimination of C. fetus subspecies, we were able to identify a proportion (85.4%) of the C. fetus-positive samples correctly as C. fetus venerealis with at least one subspecies-specific PCR, but C. fetus fetus was not detected in any of the samples tested. Remarkably, C. fetus subspecies amplification was observed following PCR on some samples (33.1%) considered C. fetus-negative, highlighting the need for rigorous criteria for discriminating between C. fetus subspecies, to improve understanding of the role of the two C. fetus subspecies in the epidemiology and pathogenesis of bovine infectious infertility.

RevDate: 2021-07-26

Martinez Boggio G, Meynadier A, Daunis-I-Estadella P, et al (2021)

Compositional analysis of ruminal bacteria from ewes selected for somatic cell score and milk persistency.

PloS one, 16(7):e0254874 pii:PONE-D-21-12205.

Ruminants are dependent on their rumen microbiota to obtain energy from plants. The composition of the microbiome was well-known to be associated with health status, and production traits, but published results are difficult to reproduce due to large sources of variation. The objectives of this study were to evaluate the associations of ruminal microbiota and its association with genetic lines selected by somatic cell score (SCS) or milk persistency (PERS), as well as milk production, somatic cell score, fat and protein contents, and fatty acids and proteins of milk, using the principles of compositional data. A large sample of 700 Lacaune dairy ewes from INRAE La Fage feeding the same diet and belonging to two divergent genetic lines selected for SCS or PERS was used. The ruminal bacterial metagenome was sequenced using the 16S rRNA gene, resulting in 2,059 operational taxonomic units affiliated with 112 genera. The abundance data were centred log-transformed after the replacement of zeros with the geometric Bayesian method. Discriminant analysis of the SCS showed differences between SCS+ and SCS- ewes, while for PERS no difference was obtained. Milk traits as fat content, protein content, saturated fatty acids and caseins of milk were negatively associated with Prevotella (R = [-0.08;-0.16]), Suttonella (R = [-0.09;-0.16]) and Ruminococcus (R = [-0.08;-0.16]), and positively associated with Lachnospiraceae (R = [0.09;0.16]) and Christensenellaceae (R = [0.09;0.16]). Our findings provide an understanding of the application of compositional data to microbiome analysis, and the potential association of Prevotella, Suttonella, Ruminococcaceae and Lachnospiraceae with milk production traits such as milk fatty acids and proteins in dairy sheep.

RevDate: 2021-07-26

Wardman JF, Rahfeld P, Liu F, et al (2021)

Discovery and Development of Promiscuous O-Glycan Hydrolases for Removal of Intact Sialyl T-Antigen.

ACS chemical biology [Epub ahead of print].

Mucin-type O-glycosylation (O-glycosylation) is a common post-translational modification that confers distinct biophysical properties to proteins and plays crucial roles in intercellular signaling. Yet, despite the importance of O-glycans, relatively few tools exist for their analysis and modification. In particular, there is a need for enzymes that can cleave the wide range of O-glycan structures found on protein surfaces, to facilitate glycan profiling and editing. Through functional metagenomic screening of the human gut microbiome, we discovered endo-O-glycan hydrolases from CAZy family GH101 that are capable of slowly cleaving the intact sialyl T-antigen trisaccharide (a ubiquitous O-glycan structure in humans) in addition to their primary activity against the T-antigen disaccharide. We then further explored this sequence space through phylogenetic profiling and analysis of representative enzymes, revealing large differences in the levels of this promiscuous activity between enzymes within the family. Through structural and sequence analysis, we identified active site residues that modulate specificity. Through subsequent rational protein engineering, we improved the activity of an enzyme identified by phylogenetic profiling sufficiently that substantial removal of the intact sialyl T-antigen from proteins could be readily achieved. Our best sialyl T-antigen hydrolase mutant, SpGH101 Q868G, is further shown to function on a number of proteins, tissues, and cells. Access to this enzyme opens up improved methodologies for unraveling the glycan code.

RevDate: 2021-07-26

Sung JY, Lee YJ, Cho YJ, et al (2021)

A Large-Scale Metagenomic Study for Enzyme Profiles Using the Focused Identification of the NGS-Based Definitive Enzyme Research (FINDER) Strategy.

Biotechnology and bioengineering [Epub ahead of print].

Excavating the molecular details of many diverse enzymes from metagenomes remains challenging in agriculture, food, health, and environmental fields. We present a versatile method that accelerates metabolic enzyme discovery for highly selective gene capture in metagenomes using next-generation sequencing. Culture-independent enzyme mining of environmental DNA is based on a set of short identifying degenerate sequences specific for a wide range of enzyme superfamilies, followed by multiplexed DNA barcode sequencing. A strategy of 'focused identification of next-generation sequencing-based definitive enzyme research' (FINDER) enabled us to generate targeted enzyme datasets from metagenomes, resulting in minimal hands-on obtention of high-throughput biological diversity and potential function profiles, without being time-consuming. This method also provided a targeted inventory of predicted proteins and molecular features of metabolic activities from several metagenomic samples. We suggest that the efficiency and sensitivity of this method will accelerate the decryption of microbial diversity and the signature of proteins and their metabolism from environmental samples. This article is protected by copyright. All rights reserved.

RevDate: 2021-07-27

Berger S, Shaw DR, Berben T, et al (2021)

Current production by non-methanotrophic bacteria enriched from an anaerobic methane-oxidizing microbial community.

Biofilm, 3:100054.

In recent years, the externalization of electrons as part of respiratory metabolic processes has been discovered in many different bacteria and some archaea. Microbial extracellular electron transfer (EET) plays an important role in many anoxic natural or engineered ecosystems. In this study, an anaerobic methane-converting microbial community was investigated with regard to its potential to perform EET. At this point, it is not well-known if or how EET confers a competitive advantage to certain species in methane-converting communities. EET was investigated in a two-chamber electrochemical system, sparged with methane and with an applied potential of +400 mV versus standard hydrogen electrode. A biofilm developed on the working electrode and stable low-density current was produced, confirming that EET indeed did occur. The appearance and presence of redox centers at -140 to -160 mV and at -230 mV in the biofilm was confirmed by cyclic voltammetry scans. Metagenomic analysis and fluorescence in situ hybridization of the biofilm showed that the anaerobic methanotroph 'Candidatus Methanoperedens BLZ2' was a significant member of the biofilm community, but its relative abundance did not increase compared to the inoculum. On the contrary, the relative abundance of other members of the microbial community significantly increased (up to 720-fold, 7.2% of mapped reads), placing these microorganisms among the dominant species in the bioanode community. This group included Zoogloea sp., Dechloromonas sp., two members of the Bacteroidetes phylum, and the spirochete Leptonema sp. Genes encoding proteins putatively involved in EET were identified in Zoogloea sp., Dechloromonas sp. and one member of the Bacteroidetes phylum. We suggest that instead of methane, alternative carbon sources such as acetate were the substrate for EET. Hence, EET in a methane-driven chemolithoautotrophic microbial community seems a complex process in which interactions within the microbial community are driving extracellular electron transfer to the electrode.

RevDate: 2021-07-27

Wang Z, He Y, Wang C, et al (2021)

Variations in Microbial Diversity and Metabolite Profiles of Female Landrace Finishing Pigs With Distinct Feed Efficiency.

Frontiers in veterinary science, 8:702931.

To enhance pig production, feed efficiency (FE) should be improved; however, the mechanisms by which gut microbes affect FE in pigs have not been fully elucidated. To investigate the differences between the composition and functionality of the gut microbiota associated with low and high FE, microbial compositions were characterized using 16S rRNA sequencing, functional annotations were performed by shotgun metagenomics, and metabolomic profiles were created by GC-TOF-MS from female Landrace finishing pigs with low and high feed conversion ratios (FCRs). Lactobacillus was enriched in the gut microbiota of individuals with low FCRs (and thus high FE), while Prevotella abundance was significantly higher in individuals with high FCRs (and thus low FE). This may be linked to carbohydrate consumption and incomplete digestion. The activity of pathways involved in the metabolism of cofactors and vitamins was greater in pigs with lower FE. We also identified differences in pyruvate-related metabolism, including phenylalanine and lysine metabolism. This suggests that pyruvate metabolism is closely related to microbial fermentation in the colon, which in turn affects glycolysis. This study deepens our understanding of how gut microbiota are related to pig growth traits, and how regulating microbial composition could aid in improving porcine FE. However, these results need to be validated using a larger pig cohort in the future.

RevDate: 2021-07-27

Shi Y, Tao J, Li B, et al (2021)

The Gut Viral Metagenome Analysis of Domestic Dogs Captures Snapshot of Viral Diversity and Potential Risk of Coronavirus.

Frontiers in veterinary science, 8:695088.

The close relations between dogs (Canis lupus familiaris) and humans lay a foundation for cross species transmissions of viruses. The co-existence of multiplex viruses in the host accelerate viral variations. For effective prediction and prevention of potential epidemic or even pandemic, the metagenomics method was used to investigate the gut virome status of 45 domestic healthy dogs which have extensive contact with human beings. A total of 248.6 GB data (505, 203, 006 valid reads, 150 bp in length) were generated and 325, 339 contigs, which were best matched with viral genes, were assembled from 46, 832, 838 reads. In the aggregate, 9,834 contigs (3.02%) were confirmed for viruses. The top 30 contigs with the most reads abundance were mapped to DNA virus families Circoviridae, Parvoviridae and Herpesviridae; and RNA virus families Astroviridae, Coronaviridae and Picornaviridae, respectively. Numerous sequences were assigned to animal virus families of Astroviridae, Coronaviridae, Circoviridae, etc.; and phage families of Microviridae, Siphoviridae, Ackermannviridae, Podoviridae, Myoviridae and the unclassified phages. Further, several sequences were homologous with the insect and plant viruses, which reflects the diet and habitation of dogs. Significantly, canine coronavirus was uniquely identified in all the samples with high abundance, and the phylogenetic analysis therefore showed close relationship with the human coronavirus strain 229E and NL63, indicating the potential risk of canine coronavirus to infect humans by obtaining the ability of cross-species transmission. This study emphasizes the high detection frequency of virus harbored in the enteric tract of healthy contacted animal, and expands the knowledge of the viral diversity and the spectrum for further disease-association studies, which is meaningful for elucidating the epidemiological and biological role of companion animals in public health.

RevDate: 2021-07-27

Liu Y, Li X, Yang Y, et al (2021)

Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing.

Frontiers in molecular biosciences, 8:703638.

The gastrointestinal tract, the largest human microbial reservoir, is highly dynamic. The gut microbes play essential roles in causing colorectal diseases. In the present study, we explored potential keystone taxa during the development of colorectal diseases in central China. Fecal samples of some patients were collected and were allocated to the adenoma (Group A), colorectal cancer (Group C), and hemorrhoid (Group H) groups. The 16S rRNA amplicon and shallow metagenomic sequencing (SMS) strategies were used to recover the gut microbiota. Microbial diversities obtained from 16S rRNA amplicon and SMS data were similar. Group C had the highest diversity, although no significant difference in diversity was observed among the groups. The most dominant phyla in the gut microbiota of patients with colorectal diseases were Bacteroidetes, Firmicutes, and Proteobacteria, accounting for >95% of microbes in the samples. The most abundant genera in the samples were Bacteroides, Prevotella, and Escherichia/Shigella, and further species-level and network analyses identified certain potential keystone taxa in each group. Some of the dominant species, such as Prevotella copri, Bacteroides dorei, and Bacteroides vulgatus, could be responsible for causing colorectal diseases. The SMS data recovered diverse antibiotic resistance genes of tetracycline, macrolide, and beta-lactam, which could be a result of antibiotic overuse. This study explored the gut microbiota of patients with three different types of colorectal diseases, and the microbial diversity results obtained from 16S rRNA amplicon sequencing and SMS data were found to be similar. However, the findings of this study are based on a limited sample size, which warrants further large-scale studies. The recovery of gut microbiota profiles in patients with colorectal diseases could be beneficial for future diagnosis and treatment with modulation of the gut microbiota. Moreover, SMS data can provide accurate species- and gene-level information, and it is economical. It can therefore be widely applied in future clinical metagenomic studies.

RevDate: 2021-07-27

Gao R, Zhu Y, Kong C, et al (2021)

Alterations, Interactions, and Diagnostic Potential of Gut Bacteria and Viruses in Colorectal Cancer.

Frontiers in cellular and infection microbiology, 11:657867.

Gut microbiome alteration was closely associated with colorectal cancer (CRC). Previous studies had demonstrated the bacteria composition changes but lacked virome profiles, trans-kindom interactions, and reliable diagnostic model explorations in CRC. Hence, we performed metagenomic sequencing to investigate the gut microbiome and microbial interactions in adenoma and CRC patients. We found the decreased microbial diversity in CRC and revealed the taxonomic alterations of bacteria and viruses were highly associated with CRC at the species level. The relative abundance of oral-derived species, such as Fusobacterium nucleatum, Fusobacterium hwasookii, Porphyromonas gingivalis, and Bacteroides fragilis, increased. At the same time, butyrate-producing and anti-inflammatory microbes decreased in adenoma and CRC by non-parametric Kruskal-Wallis test. Despite that, the relative abundance of Escherichia viruses and Salmonella viruses increased, whereas some phages, including Enterobacteria phages and Uncultured crAssphage, decreased along with CRC development. Gut bacteria was negatively associated with viruses in CRC and healthy control by correlation analysis (P=0.017 and 0.002, respectively). Viruses were much more dynamic than the bacteria as the disease progressed, and the altered microbial interactions were distinctively stage-dependent. The degree centrality of microbial interactions decreased while closeness centrality increased along with the adenoma to cancer development. Uncultured crAssphage was the key bacteriophage that enriched in healthy controls and positively associated with butyrate-producing bacteria. Diagnostic tests based on bacteria by random forest confirmed in independent cohorts showed better performance than viruses for CRC. In conclusion, our study revealed the novel CRC-associated bacteria and viruses that exhibited specific differences and intensive microbial correlations, which provided a reliable diagnostic panel for CRC.

RevDate: 2021-07-27

Wang Y, Lv X, Li X, et al (2021)

Protective Effect of Lactobacillus plantarum P8 on Growth Performance, Intestinal Health, and Microbiota in Eimeria-Infected Broilers.

Frontiers in microbiology, 12:705758.

Coccidiosis is one of the major parasitic diseases in the commercial broiler industry. Probiotics can protect poultry against Eimeria infection. However, the mechanisms are not fully known. Therefore, Lactobacillus plantarum P8 (P8) was used to investigate its anti-coccidial property and mechanism. Five hundred broilers were allocated to five treatments: control diet (NC), control diet + Eimeria infection (IC), control diet containing 1 × 107 cfu/g P8 + Eimeria infection (P8L), control diet containing 1 × 108 cfu/g P8 + Eimeria infection (P8H), and control diet + Eimeria infection + Diclazuril (DIC). At day 14, all treatments except NC were inoculated with sporulated oocysts. Results indicated that Eimeria infection increased the mortality and oocysts shedding, and declined the growth performance as well as the intestinal barrier in Eimeria-treated broilers. On the contrary, dietary supplementation of low level P8, high level P8 and DIC decreased the mortality and oocysts shedding, but improved the growth performance and intestinal barrier. The impaired intestinal morphology in the IC group was also improved by P8H and DIC treatments. Besides, the elevated oxidative stress and pro-inflammation in Eimeria-infected broilers were reduced by P8L, P8H, and DIC treatments. Metagenomic analysis indicated P8 altered the structure of the gut microbiota, and the alteration was more obvious at day 21 than day 42. Notably, IC also increased the abundances of Eimeriidae, Eimeria and Eimeria tenella at day 21, while P8L and DIC decreased the abundances. Correlation analysis revealed that bacteria in Eimeria-treated broilers positively correlated with the intestinal permeability, oxidative stress and inflammation, while bacteria in broilers receiving P8L and DIC negatively correlated with the aforementioned pathological indices. Functional prediction demonstrated that the metagenomes of Eimeria-infected broilers were involved in several diseases. But the metagenomes of P8L-treated broilers were involved in energy metabolism and replication repair. In conclusion, dietary P8 supplementation inhibited oocyst shedding and improved the growth performance as well as the intestinal health of broilers infected with Eimeria, which was closely related to the regulation of gut microbiota. Moreover, the effects of P8 may be more effective in the early infection of coccidia.

RevDate: 2021-07-27

Shim H, Shivram H, Lei S, et al (2021)

Diverse ATPase Proteins in Mobilomes Constitute a Large Potential Sink for Prokaryotic Host ATP.

Frontiers in microbiology, 12:691847.

Prokaryote mobilome genomes rely on host machineries for survival and replication. Given that mobile genetic elements (MGEs) derive their energy from host cells, we investigated the diversity of ATP-utilizing proteins in MGE genomes to determine whether they might be associated with proteins that could suppress related host proteins that consume energy. A comprehensive search of 353 huge phage genomes revealed that up to 9% of the proteins have ATPase domains. For example, ATPase proteins constitute ∼3% of the genomes of Lak phages with ∼550 kbp genomes that occur in the microbiomes of humans and other animals. Statistical analysis shows the number of ATPase proteins increases linearly with genome length, consistent with a large sink for host ATP during replication of megaphages. Using metagenomic data from diverse environments, we found 505 mobilome proteins with ATPase domains fused to diverse functional domains. Among these composite ATPase proteins, 61.6% have known functional domains that could contribute to host energy diversion during the mobilome infection cycle. As many have domains that are known to interact with nucleic acids and proteins, we infer that numerous ATPase proteins are used during replication and for protection from host immune systems. We found a set of uncharacterized ATPase proteins with nuclease and protease activities, displaying unique domain architectures that are energy intensive based on the presence of multiple ATPase domains. In many cases, these composite ATPase proteins genomically co-localize with small proteins in genomic contexts that are reminiscent of toxin-antitoxin systems and phage helicase-antibacterial helicase systems. Small proteins that function as inhibitors may be a common strategy for control of cellular processes, thus could inspire future biochemical experiments for the development of new nucleic acid and protein manipulation tools, with diverse biotechnological applications.

RevDate: 2021-07-27

Wind L, Keenum I, Gupta S, et al (2021)

Integrated Metagenomic Assessment of Multiple Pre-harvest Control Points on Lettuce Resistomes at Field-Scale.

Frontiers in microbiology, 12:683410.

An integrated understanding of factors influencing the occurrence, distribution, and fate of antibiotic resistance genes (ARGs) in vegetable production systems is needed to inform the design and development of strategies for mitigating the potential for antibiotic resistance propagation in the food chain. The goal of the present study was to holistically track antibiotic resistance and associated microbiomes at three distinct pre-harvest control points in an agroecosystem in order to identify the potential impacts of key agricultural management strategies. Samples were collected over the course of a single growing season (67 days) from field-scale plots amended with various organic and inorganic amendments at agronomic rates. Dairy-derived manure and compost amendment samples (n = 14), soil samples (n = 27), and lettuce samples (n = 12) were analyzed via shotgun metagenomics to assess multiple pre-harvest factors as hypothetical control points that shape lettuce resistomes. Pre-harvest factors of interest included manure collection during/post antibiotic use, manure composting, and soil amended with organic (stockpiled manure/compost) versus chemical fertilizer. Microbial community resistome and taxonomic compositions were unique from amendment to soil to lettuce surface according to dissimilarity analysis. The highest resistome alpha diversity (i.e., unique ARGs, n = 642) was detected in amendment samples prior to soil application, while the composted manure had the lowest total ARG relative abundance (i.e., 16S rRNA gene-normalized). Regardless of amendment type, soils acted as an apparent ecological buffer, i.e., soil resistome and taxonomic profiles returned to background conditions 67 d-post amendment application. Effects of amendment conditions surprisingly re-emerged in lettuce phyllosphere resistomes, with the highest total ARG relative abundances recovered on the surface of lettuce plants grown in organically-fertilized soils (i.e., compost- and manure-amended soils). Co-occurrence analysis identified 55 unique ARGs found both in the soil amendments and on lettuce surfaces. Among these, arnA and pmrF were the most abundant ARGs co-occurring with mobile genetic elements (MGE). Other prominent ARG-MGE co-occurrences throughout this pre-harvest lettuce production chain included: TetM to transposon (Clostridiodies difficile) in the manure amendment and TriC to plasmid (Ralstonia solanacearum) on the lettuce surfaces. This suggests that, even with imposing manure management and post-amendment wait periods in agricultural systems, ARGs originating from manure can still be found on crop surfaces. This study demonstrates a comprehensive approach to identifying key control points for the propagation of ARGs in vegetable production systems, identifying potential ARG-MGE combinations that could inform future surveillance. The findings suggest that additional pre-harvest and potentially post-harvest interventions may be warranted to minimize risk of propagating antibiotic resistance in the food chain.

RevDate: 2021-07-27

Mghazli N, Sbabou L, Hakkou R, et al (2021)

Description of Microbial Communities of Phosphate Mine Wastes in Morocco, a Semi-Arid Climate, Using High-Throughput Sequencing and Functional Prediction.

Frontiers in microbiology, 12:666936.

Soil microbiota are vital for successful revegetation, as they play a critical role in nutrient cycles, soil functions, and plant growth and health. A rehabilitation scenario of the abandoned Kettara mine (Morocco) includes covering acidic tailings with alkaline phosphate mine wastes to limit water infiltration and hence acid mine drainage. Revegetation of phosphate wastes is the final step to this rehabilitation plan. However, revegetation is hard on this type of waste in semi-arid areas and only a few plants managed to grow naturally after 5 years on the store-and-release cover. As we know that belowground biodiversity is a key component for aboveground functioning, we sought to know if any structural problem in phosphate waste communities could explain the almost absence of plants. To test this hypothesis, bacterial and archaeal communities present in these wastes were assessed by 16S rRNA metabarcoding. Exploration of taxonomic composition revealed a quite diversified community assigned to 19 Bacterial and two Archaeal phyla, similar to other studies, that do not appear to raise any particular issues of structural problems. The dominant sequences belonged to Proteobacteria, Bacteroidetes, Actinobacteria, and Gemmatimonadetes and to the genera Massilia, Sphingomonas, and Adhaeribacter. LEfSe analysis identified 19 key genera, and metagenomic functional prediction revealed a broader phylogenetic range of taxa than expected, with all identified genera possessing at least one plant growth-promoting trait. Around 47% of the sequences were also related to genera possessing strains that facilitate plant development under biotic and environmental stress conditions, such as drought and heat.

RevDate: 2021-07-26

Jia B, Han X, Kim KH, et al (2021)

Discovery and mining of enzymes from the human gut microbiome.

Trends in biotechnology pii:S0167-7799(21)00138-4 [Epub ahead of print].

Advances in technological and bioinformatics approaches have led to the generation of a plethora of human gut metagenomic datasets. Metabolomics has also provided substantial data regarding the small metabolites produced and modified by the microbiota. Comparatively, the microbial enzymes mediating the transformation of metabolites have not been intensively investigated. Here, we discuss the recent efforts and technologies used for discovering and mining enzymes from the human gut microbiota. The wealth of knowledge on metabolites, reactions, genome sequences, and structures of proteins, may drive the development of strategies for enzyme mining. Ongoing efforts to annotate gut microbiota enzymes will explain catalytic mechanisms that may guide the clinical applications of the gut microbiome for diagnostic and therapeutic purposes.

RevDate: 2021-07-27

Sepúlveda-Correa A, Daza-Giraldo LV, Polanía J, et al (2021)

Genes associated with antibiotic tolerance and synthesis of antimicrobial compounds in a mangrove with contrasting salinities.

Marine pollution bulletin, 171:112740 pii:S0025-326X(21)00774-8 [Epub ahead of print].

Salinity and wastewater pollution in mangrove ecosystems can affect microorganisms and the abundance of genes involved in response to these stressors. This research aimed to identify genes associated with resistance and biosynthesis of antimicrobial compounds in mangrove soils subjected to contrasting salinities and wastewater pollution. Samples of rhizospheric soil were taken from a mangrove at the mouth of the Ranchería River in La Guajira, Colombia. A functional analysis was performed using Illumina HiSeq 2500 sequencing data obtained from total DNA extracted. Increased salt concentration influenced metabolic pathways and differential abundance of genes associated with the synthesis of antimicrobial compounds (e.g., rfbB/rffG, INO1/ISYNA1, rfbA/rffH, sat/met3, asd). Also, among 33 genes involved in intrinsic antibiotic resistance, 16 were significantly influenced by salinity (e.g., cusR/copR/silR, vgb, tolC). We concluded that salt stress tolerance and adaptive mechanisms could favor the biosynthesis of antimicrobial compounds in mangroves contaminated by sewage.

RevDate: 2021-07-27

Dang C, Liu S, Chen Q, et al (2021)

Response of microbial nitrogen transformation processes to antibiotic stress in a drinking water reservoir.

The Science of the total environment, 797:149119 pii:S0048-9697(21)04192-9 [Epub ahead of print].

Effects of antibiotics on microbial nitrogen transformation processes in natural aquatic ecosystems are largely unknown. In this study, we utilized the 15N stable isotope tracers and metagenomic sequencing to identify how antibiotics drive nitrogen transformation processes in Danjiangkou Reservoir, which is the largest artificial drinking water reservoir in China. We retrieved 51 nitrogen functional genes, and found that the highest abundances of nitrate reduction and denitrification-related genes occurred in dissimilatory nitrogen transformation pathways. 15N-labelling analysis substantiated that denitrification was the main pathway for nitrogen removal, accounting for 57.1% of nitrogen loss. Nitrogen functional genes and antibiotic resistance genes co-occurred in Danjiangkou Reservoir, and they were mainly carried by the denitrifying bacteria such as Rhodoferax, Polaromonas, Limnohabitans, Pararheinheimera, Desulfobulbus, and Pseudopelobacter. Genome annotation revealed that antibiotic deactivation, Resistance-Nodulation-Division and facilitator superfamily efflux pumps were responsible for the multiple-resistance to antibiotics in these bacteria. Moreover, antibiotics showed non-significant effects on nitrogen transformation processes. It is speculated that denitrifying bacteria harboring ARGs played crucial roles in protecting nitrogen transformation from low-level antibiotics stress in the reservoir. Our results highlight that denitrifying bacteria are important hosts of ARGs, which provides a novel perspective for evaluating the effects of antibiotics on nitrogen cycle in natural aquatic ecosystems.

RevDate: 2021-07-26

Hyun DW, Lee JY, Kim MS, et al (2021)

Pathogenomics of Streptococcus ilei sp. nov., a newly identified pathogen ubiquitous in human microbiome.

Journal of microbiology (Seoul, Korea), 59(8):792-806.

Viridans group streptococci are a serious health concern because most of these bacteria cause life-threatening infections, especially in immunocompromised and hospitalized individuals. We focused on two alpha-hemolytic Streptococcus strains (I-G2 and I-P16) newly isolated from an ileostomy effluent of a colorectal cancer patient. We examined their pathogenic potential by investigating their prevalence in human and assessing their pathogenicity in a mouse model. We also predicted their virulence factors and pathogenic features by using comparative genomic analysis and in vitro tests. Using polyphasic and systematic approaches, we identified the isolates as belonging to a novel Streptococcus species and designated it as Streptococcus ilei. Metagenomic survey based on taxonomic assignment of datasets from the Human Microbiome Project revealed that S. ilei is present in most human population and at various body sites but is especially abundant in the oral cavity. Intraperitoneal injection of S. ilei was lethal to otherwise healthy C57BL/6J mice. Pathogenomics and in vitro assays revealed that S. ilei possesses a unique set of virulence factors. In agreement with the in vivo and in vitro data, which indicated that S. ilei strain I-G2 is more pathogenic than strain I-P16, only the former displayed the streptococcal group A antigen. We here newly identified S. ilei sp. nov., and described its prevalence in human, virulence factors, and pathogenicity. This will help to prevent S. ilei strain misidentification in the future, and improve the understanding and management of streptococcal infections.

RevDate: 2021-07-24

Dong X, Zhang C, Li W, et al (2021)

Functional diversity of microbial communities in inactive seafloor sulfide deposits.

FEMS microbiology ecology pii:6327547 [Epub ahead of print].

The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.

RevDate: 2021-07-26

Leekitcharoenphon P, Johansson MHK, Munk P, et al (2021)

Genomic evolution of antimicrobial resistance in Escherichia coli.

Scientific reports, 11(1):15108.

The emergence of antimicrobial resistance (AMR) is one of the biggest health threats globally. In addition, the use of antimicrobial drugs in humans and livestock is considered an important driver of antimicrobial resistance. The commensal microbiota, and especially the intestinal microbiota, has been shown to have an important role in the emergence of AMR. Mobile genetic elements (MGEs) also play a central role in facilitating the acquisition and spread of AMR genes. We isolated Escherichia coli (n = 627) from fecal samples in respectively 25 poultry, 28 swine, and 15 veal calf herds from 6 European countries to investigate the phylogeny of E. coli at country, animal host and farm levels. Furthermore, we examine the evolution of AMR in E. coli genomes including an association with virulence genes, plasmids and MGEs. We compared the abundance metrics retrieved from metagenomic sequencing and whole genome sequenced of E. coli isolates from the same fecal samples and farms. The E. coli isolates in this study indicated no clonality or clustering based on country of origin and genetic markers; AMR, and MGEs. Nonetheless, mobile genetic elements play a role in the acquisition of AMR and virulence genes. Additionally, an abundance of AMR was agreeable between metagenomic and whole genome sequencing analysis for several AMR classes in poultry fecal samples suggesting that metagenomics could be used as an indicator for surveillance of AMR in E. coli isolates and vice versa.

RevDate: 2021-07-26

Vicedomini R, Quince C, Darling AE, et al (2021)

Strainberry: automated strain separation in low-complexity metagenomes using long reads.

Nature communications, 12(1):4485.

High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities. Microbiomes often contain multiple strains of the same species, and different strains have been shown to have important differences in their functional roles. Recent advances on long-read based methods enabled accurate assembly of bacterial genomes from complex microbiomes and an as-yet-unrealized opportunity to resolve strains. Here we present Strainberry, a metagenome assembly pipeline that performs strain separation in single-sample low-complexity metagenomes and that relies uniquely on long-read data. We benchmarked Strainberry on mock communities for which it produces strain-resolved assemblies with near-complete reference coverage and 99.9% base accuracy. We also applied Strainberry on real datasets for which it improved assemblies generating 20-118% additional genomic material than conventional metagenome assemblies on individual strain genomes. We show that Strainberry is also able to refine microbial diversity in a complex microbiome, with complete separation of strain genomes. We anticipate this work to be a starting point for further methodological improvements on strain-resolved metagenome assembly in environments of higher complexities.

RevDate: 2021-07-24

Roodgar M, Good BH, Garud NR, et al (2021)

Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment.

Genome research pii:gr.265058.120 [Epub ahead of print].

Gut microbial communities can respond to antibiotic perturbations by rapidly altering their taxonomic and functional composition. However, little is known about the strain-level processes that drive this collective response. Here, we characterize the gut microbiome of a single individual at high temporal and genetic resolution through a period of health, disease, antibiotic treatment, and recovery. We used deep, linked-read metagenomic sequencing to track the longitudinal trajectories of thousands of single nucleotide variants within 36 species, which allowed us to contrast these genetic dynamics with the ecological fluctuations at the species level. We found that antibiotics can drive rapid shifts in the genetic composition of individual species, often involving incomplete genome-wide sweeps of pre-existing variants. These genetic changes were frequently observed in species without obvious changes in species abundance, emphasizing the importance of monitoring diversity below the species level. We also found that many sweeping variants quickly reverted to their baseline levels once antibiotic treatment had concluded, demonstrating that the ecological resilience of the microbiota can sometimes extend all the way down to the genetic level. Our results provide new insights into the population genetic forces that shape individual microbiomes on therapeutically relevant timescales, with potential implications for personalized health and disease.

RevDate: 2021-07-26

Su Mun L, Wye Lum S, Kong Yuiin Sze G, et al (2021)

Association of Microbiome with Oral Squamous Cell Carcinoma: A Systematic Review of the Metagenomic Studies.

International journal of environmental research and public health, 18(14): pii:ijerph18147224.

The past decade has witnessed a surge in epidemiological studies that have explored the relationship between the oral microbiome and oral cancer. Owing to the diversity of the published data, a comprehensive systematic overview of the currently available evidence is critical. This review summarises the current evidence on the metagenomic studies on the oral microbiome in oral cancer. A systematic search was conducted in Medline and Embase databases to identify original studies examining the differences in the oral microbiome of oral cancer cases and controls. A total of twenty-six studies were identified that reported differences in microbial abundance between oral squamous cell carcinoma (OSCC) and controls. Although almost all the studies identified microbial dysbiosis to be associated with oral cancer, the detailed qualitative analysis did not reveal the presence/abundance of any individual bacteria or a consortium to be consistently enriched in OSCC samples across the studies. Interestingly, few studies reported a surge of periodontopathogenic taxa, especially Fusobacteria, whereas others demonstrated a depletion of commensal taxa Streptococci. Considerable heterogeneity could be identified in the parameters used for designing the studies as well as reporting the microbial data. If microbiome data needs to be translated in the future, to complement the clinical parameters for diagnosis and prognosis of oral cancer, further studies with the integration of clinical variables, adequate statistical power, reproducible methods, and models are required.

RevDate: 2021-07-27

Khan KN, Fujishita A, Muto H, et al (2021)

Levofloxacin or gonadotropin releasing hormone agonist treatment decreases intrauterine microbial colonization in human endometriosis.

European journal of obstetrics, gynecology, and reproductive biology, 264:103-116 pii:S0301-2115(21)00349-3 [Epub ahead of print].

OBJECTIVE: We examined the hypothesis that antibiotic treatment with or without gonadotropin releasing hormone agonist (GnRHa) may decrease intrauterine infection with consequent decrease in tissue inflammation, cell proliferation and angiogenesis in human endometriosis.

STUDY DESIGN: This is a prospective non-randomized observational study. Endometrial/endometriotic samples were collected during surgery from 53 women with endometriosis and 47 control women who were treated with levofloxacin (LVFX, 500 mg, once per os) or GnRHa (1.88 mg/IM for 3 months) before surgery. Endometrial samples were analyzed by broad-range polymerase-chain reaction (PCR) amplification of bacteria targeting V5-V6 region of 16S rRNA gene. Immunohistochemical analysis was performed using antibodies against CD138 (Syndecan-1, a marker of plasma cells), CD68 (marker of macrophages), Ki-67 (cell proliferation marker), and CD31 (vascular cells marker).

RESULTS: 16S rDNA metagenome assay indicated that treatment with either of LVFX or GnRHa + LVFX significantly decreased some components of major bacterial genera comparing to untreated group. In women with endometriosis, treatment with either of LVFX or GnRHa + LVFX significantly decreased Gardnerella, Prevotella, Acidibactor, Atopobium, Megasphaera, and Bradyrhizobium (p < 0.05 for each) comparing to untreated group. Cochran-Mantel-Haenszel test indicated that occurrence rate of chronic endometritis was significantly decreased after GnRHa + LVFX treatment comparing to GnRHa treatment group (p = 0.041). These findings were coincided with significantly decreased CD68-stained macrophage infiltration, Ki-67- stained cell proliferation and CD31-stained micro-vessel density in endometria and endometriotic lesions with histology proven improvement in the morphological appearance of ovarian endometrioma.

CONCLUSIONS: These findings suggest that clinical administration of a broad-spectrum antibiotic with or without GnRHa may be effective in improving uterine infection with decrease of tissue inflammation, cell proliferation, and angiogenesis in human endometriosis.

RevDate: 2021-07-27

Bombaywala S, Purohit HJ, NA Dafale (2021)

Mobility of antibiotic resistance and its co-occurrence with metal resistance in pathogens under oxidative stress.

Journal of environmental management, 297:113315 pii:S0301-4797(21)01377-3 [Epub ahead of print].

The bacterial communities are challenged with oxidative stress during their exposure to bactericidal antibiotics, metals, and different levels of dissolved oxygen (DO) encountered in diverse environmental habitats. The frequency of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) co-selection is increased by selective pressure posed by oxidative stress. Hence, study of resistance acquisition is important from an evolutionary perspective. To understand the dependence of oxidative stress on the dissemination of ARGs and MRGs through a pathogenic bacterial population, 12 metagenomes belonging to gut, water and soil habitats were evaluated. The metagenome-wide analysis showed the chicken gut to pose the most diverse pool of ARGs (30.4 ppm) and pathogenic bacteria (Simpson diversity = 0.98). The most common types of resistances found in all the environmental samples were efflux pumps (13.22 ppm) and genes conferring resistance to vancomycin (12.4 ppm), tetracycline (12.1 ppm), or beta-lactam (9.4 ppm) antibiotics. Additionally, limiting DO level in soil was observed to increase the abundance of excision nucleases (uvrA and uvrB), DNA polymerase (polA), catalases (katG), and other oxidative stress response genes (OSGs). This was further evident from major variations occurred in antibiotic efflux genes due to the effect of DO concentration on two human pathogens, namely Salmonella enterica and Shigella sonnei found in all the selected habitats. In conclusion, the microbial community, when challenged with oxidative stress caused by environmental variations in oxygen level, tends to accumulate higher amounts of ARGs with increased dissemination potential through triggering non-lethal mutagenesis. Furthermore, the genetic linkage or co-occurrence of ARGs and MRGs provides evidence for selecting ARGs under high concentrations of heavy metals.

RevDate: 2021-07-24

Michel C, Raimo M, Lazarevic V, et al (2021)

Case Report: About a Case of Hyperammonemia Syndrome Following Lung Transplantation: Could Metagenomic Next-Generation Sequencing Improve the Clinical Management?.

Frontiers in medicine, 8:684040.

Background: Mycoplasma hominis and Ureaplasma spp. are responsible for opportunistic infections in transplant patients, sometimes causing a life-threatening hyperammonemia syndrome. Both pathogens are not identified with standard microbiology techniques, resulting in missed or delayed diagnosis. We present a clinical case that illustrates the added value that next-generation sequencing (NGS) may offer in the diagnosis of respiratory infections in immune-compromised patients. Results: A 55 years-old man with idiopathic pulmonary fibrosis underwent double lung transplantation. He received antibiotic prophylaxis with piperacillin-tazobactam and azythromycin. At day 4 post-transplantation (PTx), the patient presented an acute respiratory distress. A broncho-alveolar lavage (BAL) was performed. At day 5 PTx, the patient presented a status epilepticus due to diffuse cerebral oedema. Serum ammonia concentration was 661 μg/dL. BAL bacterial culture was negative. Because of the clinical presentation, special cultures were performed and identified 100.000 CFU/mL of M. hominis and Ureaplasma spp. and specific PCRs were positive for M. hominis and Ureaplasma parvum. Antibiotic therapy was shifted to therapeutic dose of azithromycin and doxycycline; within 48 h ammonia serum concentrations returned to normal but the coma persisted several weeks, followed by a persistent frontal lobe syndrome. A follow-up BAL was performed on day 11 Ptx. The Mycoplasma/Ureaplasma culture was negative, yet the specific PCRs remained positive. Bacterial culture found 100 CFU/mL of Staphylococcus aureus and viral culture was positive for Herpes Simplex Virus-1. These results were confirmed by metagenomic next-generation sequencing (mNGS). In the bacterial fraction, the majority of reads belonged to Corynebacterium propinquum (34.7%), S. aureus (24.1%) and Staphylococcus epidermidis (17.1%). Reads assigned to M. hominis, Ureaplasma urealyticum and parvum represented 0.71, 0.13, and 0.04% of the bacterial fraction and corresponded to 6.9 × 103, 9.7 × 102, and 3.7 × 102 genome equivalents per mL of BAL fluid, respectively. These results are in favor of a cure of the atypical infection. Conclusions: mNGS offered added diagnostic and quantitative values compared to PCR tests, which can remain positive after resolved infections. The initiation of appropriate antibiotic therapy would have occurred earlier on, possibly resulting in a better clinical outcome if mNGS had been performed in a routine fashion.

RevDate: 2021-07-24

Agarwal N, Rai AK, SP Singh (2021)

Biotransformation of hydroquinone into α-arbutin by transglucosylation activity of a metagenomic amylosucrase.

3 Biotech, 11(8):362.

Arbutin is a naturally occurring glycosylated product of hydroquinone. With the ability to interrupt melanin biosynthesis in epidermal cells, it is a promising cosmetic ingredient. In this study, a novel amylosucrase, Asmet, identified from a thermal spring metagenome, has been characterized for arbutin biosynthesis. Asmet was able to catalyze transglucosylation of hydroquinone to arbutin, taking sucrose as glycosyl donor, in the temperature range of 20 °C to 40 °C and pH 5.0 to 6.0, with the relative activity of 80% or more. The presence of chloride salts of Li, K, and Na at 1 mM concentration did not exhibit any notable effect on the enzyme's activity, unlike Cu, Ni, and Mn, which were observed to be detrimental. The hydroquinone (20 mM) to sucrose ratio of 1:1 to 1:10 was appropriate for the catalytic biosynthesis of arbutin. The maximum hydroquinone to arbutin conversion of 70% was obtained in 24 h of Asmet led catalysis, at 30 °C and pH 6.0. Arbutin production was also demonstrated using low-cost feedstock, table sugar, muscovado, and sweet sorghum stalk extract, as a replacement for sucrose. Whole-cell catalysis of hydroquinone to arbutin transglucosylation was also established.

RevDate: 2021-07-24

Alessia E, Medina M, William R, et al (2020)

Factors associated with elevated levels of antibiotic resistance genes in sewer sediments and wastewater.

Environmental science : water research & technology, 6(6):1697-1710.

The sewer environment is a potential hotspot for the proliferation of antibiotic resistance genes (ARGs) and other hazardous microbial agents. Understanding the potential for ARG proliferation and retardation and/or accumulation in sewer sediments is of interest for protecting the health of sewage workers and the broader community in the event of sewer overflows as well as for interpreting sewage epidemiology data. To better understand this understudied environment for antibiotic resistance, a field survey was conducted to identify the factors that may control ARGs in sewer sediments and sewage. qPCR was performed for select ARGs and amplicon sequencing was performed for paired samples from combined and separate sanitary sewer systems. Metagenomic sequencing was performed on combined sewer sediments. The relative abundances of sul1, tet(O), tet(W), ermF, and vanA were higher in wastewater compared to sewer sediments, while NDM-1 was greater in sewer sediment and ermF was similar between the two matrices. NDM-1 was observed in sewer sediment but rarely above detection in wastewater in this study. This may indicate that larger/more frequent wastewater samples are needed for detection and/or that retardation and/or accumulation in sewage sediment may need to be considered when interpreting wastewater-based epidemiology data for ARGs. Random forest analyses indicated that season and conductivity were important variables and to a lesser extent so were pH, TSS, heavy metals, and sewer type for explaining the variance of the ARGs. These variables explained the 19-61% of the variance of sul1, tet(O), tet(G), and tet(W) quantified in wastewater. These variables performed less well for explaining the variance in sewer sediments (0.2-24%). Sewer sediment and wastewater had distinct microbial community structures and biomarkers for each are described. Metagenomics indicated that a high diversity of ARGs, including several of medical importance, were observed in the combined sewer sediment. This work provides insight into the complex sewer microbiome and the potential hazard posed by different sewer matrices.

RevDate: 2021-07-24

Ziegelhöfer A, K Kujala (2021)

Assessing the Diversity and Metabolic Potential of Psychrotolerant Arsenic-Metabolizing Microorganisms From a Subarctic Peatland Used for Treatment of Mining-Affected Waters by Culture-Dependent and -Independent Techniques.

Frontiers in microbiology, 12:648412.

Arsenic contamination in water by natural causes or industrial activities is a major environmental concern, and treatment of contaminated waters is needed to protect water resources and minimize the risk for human health. In mining environments, treatment peatlands are used in the polishing phase of water treatment to remove arsenic (among other contaminants), and peat microorganisms play a crucial role in arsenic removal. The present study assessed culture-independent diversity obtained through metagenomic and metatranscriptomic sequencing and culture-dependent diversity obtained by isolating psychrotolerant arsenic-tolerant, arsenite-oxidizing, and arsenate-respiring microorganisms from a peatland treating mine effluent waters of a gold mine in Finnish Lapland using a dilution-to-extinction technique. Low diversity enrichments obtained after several transfers were dominated by the genera Pseudomonas, Polaromonas, Aeromonas, Brevundimonas, Ancylobacter, and Rhodoferax. Even though maximal growth and physiological activity (i.e., arsenite oxidation or arsenate reduction) were observed at temperatures between 20 and 28°C, most enrichments also showed substantial growth/activity at 2-5°C, indicating the successful enrichments of psychrotolerant microorganisms. After additional purification, eight arsenic-tolerant, five arsenite-oxidizing, and three arsenate-respiring strains were obtained in pure culture and identified as Pseudomonas, Rhodococcus, Microbacterium, and Cadophora. Some of the enriched and isolated genera are not known to metabolize arsenic, and valuable insights on arsenic turnover pathways may be gained by their further characterization. Comparison with phylogenetic and functional data from the metagenome indicated that the enriched and isolated strains did not belong to the most abundant genera, indicating that culture-dependent and -independent methods capture different fractions of the microbial community involved in arsenic turnover. Rare biosphere microorganisms that are present in low abundance often play an important role in ecosystem functioning, and the enriched/isolated strains might thus contribute substantially to arsenic turnover in the treatment peatland. Psychrotolerant pure cultures of arsenic-metabolizing microorganisms from peatlands are needed to close the knowledge gaps pertaining to microbial arsenic turnover in peatlands located in cold climate regions, and the isolates and enrichments obtained in this study are a good starting point to establish model systems. Improved understanding of their metabolism could moreover lead to their use in biotechnological applications intended for bioremediation of arsenic-contaminated waters.

RevDate: 2021-07-26
CmpDate: 2021-07-26

Zhang Z, L Zhang (2021)

METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs.

BMC bioinformatics, 22(Suppl 10):378.

BACKGROUND: Due to the complexity of microbial communities, de novo assembly on next generation sequencing data is commonly unable to produce complete microbial genomes. Metagenome assembly binning becomes an essential step that could group the fragmented contigs into clusters to represent microbial genomes based on contigs' nucleotide compositions and read depths. These features work well on the long contigs, but are not stable for the short ones. Contigs can be linked by sequence overlap (assembly graph) or by the paired-end reads aligned to them (PE graph), where the linked contigs have high chance to be derived from the same clusters.

RESULTS: We developed METAMVGL, a multi-view graph-based metagenomic contig binning algorithm by integrating both assembly and PE graphs. It could strikingly rescue the short contigs and correct the binning errors from dead ends. METAMVGL learns the two graphs' weights automatically and predicts the contig labels in a uniform multi-view label propagation framework. In experiments, we observed METAMVGL made use of significantly more high-confidence edges from the combined graph and linked dead ends to the main graph. It also outperformed many state-of-the-art contig binning algorithms, including MaxBin2, MetaBAT2, MyCC, CONCOCT, SolidBin and GraphBin on the metagenomic sequencing data from simulation, two mock communities and Sharon infant fecal samples.

CONCLUSIONS: Our findings demonstrate METAMVGL outstandingly improves the short contig binning and outperforms the other existing contig binning tools on the metagenomic sequencing data from simulation, mock communities and infant fecal samples.

RevDate: 2021-07-26
CmpDate: 2021-07-26

Yuan X, Zhang X, Liu X, et al (2021)

Comparison of Gut Bacterial Communities of Grapholita molesta (Lepidoptera: Tortricidae) Reared on Different Host Plants.

International journal of molecular sciences, 22(13):.

Intestinal symbiotic bacteria have played an important role in the digestion, immunity detoxification, mating, and reproduction of insects during long-term coevolution. The oriental fruit moth, Grapholita molesta, is an important fruit tree pest worldwide. However, the composition of the G. molesta microbial community, especially of the gut microbiome, remains unclear. To explore the differences of gut microbiota of G. molesta when reared on different host plants, we determined the gut bacterial structure when G. molesta was transferred from an artificial diet to different host plants (apples, peaches, nectarines, crisp pears, plums, peach shoots) by amplicon sequencing technology. The results showed that Proteobacteria and Firmicutes are dominant in the gut microbiota of G. molesta. Plum-feeding G. molesta had the highest richness and diversity of gut microbiota, while apple-feeding G. molesta had the lowest. PCoA and PERMANOVA analysis revealed that there were significant differences in the gut microbiota structure of G. molesta on different diets. PICRUSt2 analysis indicated that most of the functional prediction pathways were concentrated in metabolic and cellular processes. Our results confirmed that gut bacterial communities of G. molesta can be influenced by host diets and may play an important role in host adaptation.

RevDate: 2021-07-23
CmpDate: 2021-07-23

Karimi K, Ngoc Do D, Sargolzaei M, et al (2021)

Population Genomics of American Mink Using Whole Genome Sequencing Data.

Genes, 12(2):.

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

RevDate: 2021-07-26
CmpDate: 2021-07-26

Keehnen NLP, Fors L, Järver P, et al (2021)

A Population Genomic Investigation of Immune Cell Diversity and Phagocytic Capacity in a Butterfly.

Genes, 12(2):.

Insects rely on their innate immune system to successfully mediate complex interactions with their internal microbiota, as well as the microbes present in the environment. Given the variation in microbes across habitats, the challenges to respond to them are likely to result in local adaptations in the immune system. Here we focus upon phagocytosis, a mechanism by which pathogens and foreign particles are engulfed in order to be contained, killed, and processed. We investigated the phenotypic and genetic variation related to phagocytosis in two allopatric populations of the butterfly Pieris napi. Populations were found to differ in their hemocyte composition and overall phagocytic capability, driven by the increased phagocytic propensity of each cell type. Yet, genes annotated to phagocytosis showed no large genomic signal of divergence. However, a gene set enrichment analysis on significantly divergent genes identified loci involved in glutamine metabolism, which recently have been linked to immune cell differentiation in mammals. Together these results suggest that heritable variation in phagocytic capacity arises via a quantitative trait architecture with variation in genes affecting the activation and/or differentiation of phagocytic cells, suggesting them as potential candidate genes underlying these phenotypic differences.

RevDate: 2021-07-26
CmpDate: 2021-07-26

Akıl C, Kitaoku Y, Tran LT, et al (2021)

Mythical origins of the actin cytoskeleton.

Current opinion in cell biology, 68:55-63.

The origin of the eukaryotic cell is one of the greatest mysteries in modern biology. Eukaryotic-wide specific biological processes arose in the lost ancestors of eukaryotes. These distinctive features, such as the actin cytoskeleton, define what it is to be a eukaryote. Recent sequencing, characterization, and isolation of Asgard archaea have opened an intriguing window into the pre-eukaryotic cell. Firstly, sequencing of anaerobic sediments identified a group of uncultured organisms, Asgard archaea, which contain genes with homology to eukaryotic signature genes. Secondly, characterization of the products of these genes at the protein level demonstrated that Asgard archaea have related biological processes to eukaryotes. Finally, the isolation of an Asgard archaeon has produced a model organism in which the morphological consequences of the eukaryotic-like processes can be studied. Here, we consider the consequences for the Asgard actin cytoskeleton and for the evolution of a regulated actin system in the archaea-to-eukaryotic transition.

RevDate: 2021-07-22

Yanlong C, Kejian Y, Yin Y, et al (2021)

Reductive soil disinfestation attenuates antibiotic resistance genes in greenhouse vegetable soils.

Journal of hazardous materials, 420:126632 pii:S0304-3894(21)01597-1 [Epub ahead of print].

Reductive soil disinfestation (RSD) is an emerging technique that ameliorates soil degradation, but its effects against antibiotic resistance genes (ARGs) were unclear. Here, we examined soil properties, ARG types and numbers, and ARG profiles, and bacterial community compositions following 4 soil treatments: control; straw addition (SA); water flooding (WF); and RSD, both straw addition and water flooding. The results showed that the numbers of ARG types and subtypes decreased by 10.8% and 21.1%, respectively, after RSD, and the numbers of ARGs decreased by 18.6%. The attenuated multidrug, beta-lactam, macrolide, and phenicol resistance genes in the RSD soil corresponded to a decreased relative abundance of ARG subtypes (i.e., adeF, mdtM, TypeB_NfxB, mecA, nalC, OXA-60, and cmlA4). Taxa in phyla Proteobacteria, Actinobacteria, and Deinococcus-Thermus were the main hosts for dominant ARG subtypes and were inhibited by RSD. The selected bacterial genera and soil properties explained 83.4% of the variance in ARG composition, suggesting that the improved soil properties and the reduced potential ARG hosts produced by the interactions of straw addition and water flooding are likely responsible for ARG attenuation by RSD. Therefore, RSD has the potential to mitigate ARG pollution in soils.

RevDate: 2021-07-22

Greninger AL (2021)

Unbiased Pandemic Pathogen Detection and the Federal Register.

While I agree with much of what was written in Dr. Kumeren Govender's commentary on how metagenomics will improve diagnostics and catch early pandemics ("Precision Pandemic Preparedness: Improving Diagnostics with Metagenomics"), significant attention to current regulatory matters is required before realizing the author's vision (1).….

RevDate: 2021-07-22

Tomida S, Kitagawa S, Kandori H, et al (2021)

Inverse Hydrogen-Bonding Change Between the Protonated Retinal Schiff Base and Water Molecules upon Photoisomerization in Heliorhodopsin 48C12.

The journal of physical chemistry. B [Epub ahead of print].

Heliorhodopsin (HeR) is a new class of the rhodopsin family discovered in 2018 through functional metagenomic analysis (named 48C12). Similar to typical microbial rhodopsins, HeR possesses seven transmembrane (TM) α-helices and an all-trans-retinal covalently bonded to the lysine residue on TM7 via a protonated Schiff base. Remarkably, the HeR membrane topology is inverted compared with that of typical microbial rhodopsins. The X-ray crystal structure of HeR 48C12 was elucidated after the first report on a HeR variant from Thermoplasmatales archaeon SG8-52-1, which revealed the water-mediated hydrogen-bonding network connected to the Schiff base region in the cytoplasmic side. Herein, low-temperature light-induced FTIR spectroscopic analyses of HeR 48C12 and 15N isotopically labeled proteins were used to elucidate the structural changes during retinal photoisomerization. N-D stretching vibrations of the protonated retinal Schiff base (PRSB) at 2286 and 2302 cm-1 in the dark state, and 2239 and 2252 cm-1 in the K intermediate were observed. The frequency changes indicated that the hydrogen bond of PRSB strengthens upon photoisomerization in HeR. Moreover, O-D stretching vibration frequencies of the internal water molecules indicate that the hydrogen-bonding strength decreases concomitantly. Therefore, the PRSB hydrogen bond responds to photoisomerization in an opposite way to the hydrogen-bonding network involving water molecules. No frequency changes of the indole N-H or N-D stretching vibrations of tryptophan residues were observed upon photoisomerization, suggesting that all tryptophan residues in the HeR 48C12 maintained the hydrogen-bonding strengths in the K intermediate. These results provide insights into the molecular mechanism of the energy storage and propagation upon retinal photoisomerization in HeR.

RevDate: 2021-07-22

Bai Y, Ruan X, Li R, et al (2021)

Metagenomics-based antibiotic resistance genes diversity and prevalence risk revealed by pathogenic bacterial host in Taihu Lake, China.

Environmental geochemistry and health [Epub ahead of print].

In recent decades, antibiotics and antibiotic resistance genes (ARGs) have been regarded as emerging pollutants. In Taihu Lake, as a typical representative of freshwater system in China, the ARGs occurrence and abundance was of great importance for ecological risk control and public health protection. In this research, high-throughput sequencing and metagenomics technique were used to investigate the seasonal ARGs profile in overlying water and sediment at typical area of Taihu Lake. Besides, taxonomy pattern of ARGs host bacteria and potential pathogens were identified. The results showed that 33 ARG subtypes and 11 ARG types were detected in research area, among which bacitracin, multidrug and sulfonamides resistance gene were with the highest abundance. The relative abundance of ARGs in overlying water and sediment ranged from 1.68 to 661.05 ppm and from 1.93 to 49.47 ppm, respectively. ARG host (18 bacteria genus) were identified and annotated, among which Clostridium botulinum, Pseudomonas aeruginosa and Klebsiella pneumonia were pathogenic bacteria. The pathogens were mostly detected at Xukou Bay in spring and fall, which might be caused by the inlet water from aquaculture area of Yangcheng Lake. Pseudomonas was the most abundant ARGs host (ant2ib, baca, bl2d_oxa2,mexb, mexf, mexw and oprn), which may facilitate the propagation of ARGs in freshwater system.

RevDate: 2021-07-22

Carvalho Costa L, Stevens K, Hu X, et al (2021)

Identification and characterization of a novel virus associated with an eriophyid mite in extracts of fruit trees leaves.

Archives of virology [Epub ahead of print].

Eriophyid mites are commonly found on the leaf surface of different plant species. In the present study, a novel virus associated with an eriophyid mite species was detected using high-throughput sequencing (HTS) of total RNA from fruit tree leaves, primarily growing under greenhouse conditions. The complete genome sequence was characterized using rapid amplification of cDNA ends followed by Sanger sequencing, revealing a genome of 8885 nucleotides in length. The single positive-stranded RNA genome was predicted to encode typical conserved domains of members of the genus Iflavirus in the family Iflaviridae. Phylogenetic analysis showed this virus to be closely related to the unclassified iflavirus tomato matilda associated virus (TMaV), with a maximum amino acid sequence identity of 59% in the RNA-dependent RNA polymerase domain. This low identity value justifies the recognition of the novel virus as a potential novel iflavirus. In addition to a lack of graft-transmissibility evidence, RT-PCR and HTS detection of this virus in the putative host plants were not consistent through different years and growing seasons, raising the possibility that rather than a plant virus, this was a virus infecting an organism associated with fruit tree leaves. Identification of Tetra pinnatifidae HTS-derived contigs in all fruit tree samples carrying the novel virus suggested this mite as the most likely host of the new virus (p-value < 1e-11), which is tentatively named "eriophyid mite-associated virus" (EMaV). This study highlights the importance of a careful biological study before assigning a new virus to a particular plant host when using metagenomics data.

RevDate: 2021-07-22

Lundberg DS, Pramoj Na Ayutthaya P, Strauß A, et al (2021)

Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition.

eLife, 10: pii:66186 [Epub ahead of print].

The ratio of microbial population size relative to the amount of host tissue, or 'microbial load', is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing, add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.

RevDate: 2021-07-22

Nde AL, Charimba G, Hitzeroth A, et al (2021)

Chryseobacterium pennae sp. nov., isolated from poultry feather waste.

International journal of systematic and evolutionary microbiology, 71(7):.

A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming, aerobic, yellow-pigmented bacterium was isolated from chicken feather waste collected from an abattoir in Bloemfontein, South Africa. A polyphasic taxonomy study was used to describe and name the bacterial isolate, strain 1_F178T. The 16S rRNA gene sequence analysis and sequence comparison data indicated that strain 1_F178T was a member of the genus Chryseobacterium and was closely related to Chryseobacterium jejuense (99.1%) and Chryseobacterium nakagawai (98.7%). Overall genome similarity metrics (average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity) revealed greatest similarity to the C. jejuense and C. nakagawai type strains but were below the threshold for species delineation. Genome sequencing revealed a genome size of 6.18 Mbp and a G+C content of 35.6 mol%. The major respiratory quinone and most abundant polar lipid of strain 1_F178T were menaquinone-6 and phosphatidylethanolamine, respectively. Strain 1_F178T had a typical fatty acid composition for Chryseobacterium species. On the basis of physiological, genotypic, phylogenetic and chemotaxonomic data, strain 1_F178T constitutes a novel species of Chryseobacterium, for which the name Chryseobacterium pennae sp. nov. is proposed. The type strain is 1_F178T (=LMG 30779T=KCTC 62759T).

RevDate: 2021-07-22

Dextro RB, Delbaje E, Cotta SR, et al (2021)

Trends in free-access genomic data accelerate advances in cyanobacteria taxonomy1.

Journal of phycology [Epub ahead of print].

Free access databases of DNA sequences containing microbial genetic information have changed the way scientists look at the microbial world. Currently, the NCBI database includes about 516 distinct search results for Cyanobacteria genomes distributed in a taxonomy based on a polyphasic approach. While their classification and taxonomic relationships are widely used as it is, recent proposals to alter their grouping include further exploring the relationship between Cyanobacteria and Melainabacteria. Nowadays, most cyanobacteria still are named under the Botanical Code, however, there is a proposal made by the Genome Taxonomy Database (GTDB) to harmonize cyanobacteria nomenclature with the other bacteria, an initiative to standardize microbial taxonomy based on genome phylogeny, in order to contribute to an overall better phylogenetic resolution of microbiota. Furthermore, the assembly level of the genomes and their geographical origin demonstrates some trends of cyanobacteria genomics on the scientific community, such as low availability of complete genomes and underexplored sampling locations. By describing how the available cyanobacteria genomes from free-access databases fit within different taxonomy classifications, this review provides a holistic view of the current knowledge of cyanobacteria and indicates some steps towards improving our efforts to create a more cohesive and inclusive future classifying system, which can be greatly improved by using large scale sequencing and metagenomic techniques.

RevDate: 2021-07-22

Koczorski P, Furtado BU, Gołębiewski M, et al (2021)

The Effects of Host Plant Genotype and Environmental Conditions on Fungal Community Composition and Phosphorus Solubilization in Willow Short Rotation Coppice.

Frontiers in plant science, 12:647709.

Phosphorus (P) is an essential plant nutrient. Low availability of P in soil is mainly caused by high content of Fe2O3 in the clay fraction that binds to P making it unavailable. Beneficial microbes, such as P solubilizing microorganisms can increase the available P in soil and improve plant growth and productivity. In this study, we evaluated the effects of environmental conditions (climate, soil parameters), plant genotype, and level of plant association (rhizosphere or endophytic root organism) on the abundance and diversity of phosphorus solubilizing microorganisms in a Salix production system. We hypothesized that a lower number of endophytic fungi may possess the ability to solubilize P compared to the number of rhizosphere fungi with the same ability. We also expect that the plant genotype and the experimental site with its environmental conditions will influence fungal diversity. Two Salix genotypes grown in pure and mixed cultures were investigated for their fungal microbiome community and diversity in the rhizosphere and endosphere during two growing seasons. We found that the rhizosphere fungal community was more diverse. A general dominance of Ascomycota (Dothideomycetes) and Basidiomycota (Tremellomycetes) was observed. The classes Agaricomycetes and Pezizomycetes were more frequent in the endosphere, while Tremellomycetes and Mortierellomycetes were more abundant in the rhizosphere. Plot-specific soil properties (pH, total organic carbon, and nitrogen) significantly influenced the fungal community structure. Among the culturable fungal diversities, 10 strains of phosphate solubilizing fungi (PSFs) from roots and 12 strains from rhizosphere soil were identified using selective media supplemented with di-calcium and tri-calcium phosphates. The fungal density and the number of PSF were much higher in the rhizosphere than in the endosphere. Penicillium was the dominant genus of PSF isolated from both sites; other less frequent genera of PSFs were Alternaria, Cladosporium, and Clonostachys. Overall the main factors controlling the fungal communities (endophytic vs. rhizosphere fungi) were the soil properties and level of plant association, while no significant influence of growing season was observed. Differences between Salix genotypes were observed for culturable fungal diversity, while in metagenomic data analysis, only the class Dothideomycetes showed a significant effect from the plant genotype.

RevDate: 2021-07-22

de la Cruz Peña MJ, Gonzalez-Granado LI, Garcia-Heredia I, et al (2021)

Minimal-moderate variation of human oral virome and microbiome in IgA deficiency.

Scientific reports, 11(1):14913.

Immunoglobulin A (IgA) is the dominant antibody found in our mucosal secretions and has long been recognized to play an important role in protecting our epithelium from pathogens. Recently, IgA has been shown to be involved in gut homeostatic regulation by 'recognizing' and shaping our commensal microbes. Paradoxically, yet selective IgA-deficiency is often described as asymptomatic and there is a paucity of studies only focused on the mice and human gut microbiome context fully ignoring other niches of our body and our commensal viruses. Here, we used as a model the human oral cavity and employed a holistic view and studied the impact of IgA deficiency and also common variable IgA and IgM immunodeficiencies (CVID), on both the human virome and microbiome. Unexpectedly, metagenomic and experimental data in human IgA deficiency and CVID indicate minimal-moderate changes in microbiome and virome composition compared to healthy control group and point out to a rather functional, resilient oral commensal viruses and microbes. However, a significant depletion (two fold) of bacterial cells (p-value < 0.01) and viruses was observed in IgA-deficiency. Our results demonstrate that, within the limits of our cohort, IgA role is not critical for maintaining a rather functional salivary microbiome and suggest that IgA is not a major influence on the composition of abundant commensal microbes.

RevDate: 2021-07-22

Sun S, Zhu X, Huang X, et al (2021)

On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples.

Scientific reports, 11(1):14828.

The gut microbiota plays an important role in human health and disease. Stool, rectal swab and rectal mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. In this study, we report differences in stool, rectal swab and rectal mucosal tissue microbial communities with shotgun metagenome sequencing of 1397 stool, swab and mucosal tissue samples from 240 participants. The taxonomic composition of stool and swab samples was distinct, but less different to each other than mucosal tissue samples. Functional profile differences between stool and swab samples are smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or rectal swab gave broadly significantly correlated results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for determination of how inference can change for taxa and pathways depending on the choice of where to sample within the human gut.

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RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.

Administrator

Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.

Technologist

Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.

Facilitator

Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

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