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Metagenomic sequencing provides a culture-independent avenue to investigate the complex microbial communities by constructing metagenome-assembled genomes (MAGs). A MAG represents a ...microbial genome by a group of sequences from genome assembly with similar characteristics. It enables us to identify novel species and understand their potential functions in a dynamic ecosystem. Many computational tools have been developed to construct and annotate MAGs from metagenomic sequencing, however, there is a prominent gap to comprehensively introduce their background and practical performance. In this paper, we have thoroughly investigated the computational tools designed for both upstream and downstream analyses, including metagenome assembly, metagenome binning, gene prediction, functional annotation, taxonomic classification, and profiling. We have categorized the commonly used tools into unique groups based on their functional background and introduced the underlying core algorithms and associated information to demonstrate a comparative outlook. Furthermore, we have emphasized the computational requisition and offered guidance to the users to select the most efficient tools. Finally, we have indicated current limitations, potential solutions, and future perspectives for further improving the tools of MAG construction and annotation. We believe that our work provides a consolidated resource for the current stage of MAG studies and shed light on the future development of more effective MAG analysis tools on metagenomic sequencing.
The aim of this research was to determine the microbiota of commercial kefir, koumiss and homemade kefir samples using metagenomic analysis and compare some probiotic properties of lactic acid ...bacteria isolated from these beverages and Lactobacillus casei, used in yakult production. One koumiss, 5 commercially available kefir beverages with different brands, and 1 homemade kefir were used as samples. Microbial diversity of kefir and koumiss samples were determined by metagenomic analysis, targeting V1-V2 region of 16S rRNA gene. Streptococcus thermophilus and Lactococcus lactis were detected as dominant in direct DNA isolation from commercially available kefir beverages. Lc. lactis and Leuconostoc mesenteroides were dominant in MRS agars, and Lc. lactis were dominant in M17 agars. In kefir beverages produced by kefir grains, Lb. kefiranofaciens was determined as the dominant bacteria. Lb. kefiri and Enterococcus durans were found dominant in MRS and M17 agars respectively. Lb. kefiranofaciens, Lb. kefiri, and Str. thermophilus were the dominant bacterias of koumiss beverages. Microorganisms isolated from kefir and koumiss beverages were found to exhibit basic probiotic properties, similar to the lactic acid bacteria isolated from yakult. This research presented bacterial microflora and probiotic properties of lactic acid bacteria isolated from kefir and koumiss beverages consumed in Turkey.
The aim of this research was to determine the microbiota of commercial kefir, koumiss and homemade kefir samples using metagenomic analysis and compare some probiotic properties of lactic acid ...bacteria isolated from these beverages and Lactobacillus casei, used in yakult production. One koumiss, 5 commercially available kefir beverages with different brands, and 1 homemade kefir were used as samples. Microbial diversity of kefir and koumiss samples were determined by metagenomic analysis, targeting V1-V2 region of 16S rRNA gene. Streptococcus thermophilus and Lactococcus lactis were detected as dominant in direct DNA isolation from commercially available kefir beverages. Lc. lactis and Leuconostoc mesenteroides were dominant in MRS agars, and Lc. lactis were dominant in M17 agars. In kefir beverages produced by kefir grains, Lb. kefiranofaciens was determined as the dominant bacteria. Lb. kefiri and Enterococcus durans were found dominant in MRS and M17 agars respectively. Lb. kefiranofaciens, Lb. kefiri, and Str. thermophilus were the dominant bacterias of koumiss beverages. Microorganisms isolated from kefir and koumiss beverages were found to exhibit basic probiotic properties, similar to the lactic acid bacteria isolated from yakult. This research presented bacterial microflora and probiotic properties of lactic acid bacteria isolated from kefir and koumiss beverages consumed in Turkey.
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•Reads-based and assembly-based approaches allowed the identification of AMR genes.•Enterobacter, Acinetobacter, Escherichia and Pseudomonas harbored most of AMR genes.•MAGs and ...mobile genetic elements were reconstructed and investigated.
In the present context of growing antimicrobial resistance (AMR) concern, understanding the distribution of AMR determinants in food matrices such as milk is crucial to protect consumers and maintain high food safety standards. Herein, the resistome of different dairy farms was investigated through a shotgun metagenomic sequencing approach, taking advantage of in-line milk filters as promising tools. The application of both the reads-based and the assembly-based approaches has allowed the identification of numerous AMR determinants, enabling a comprehensive resolution of the resistome. Notably most of the species harboring AMR genes were predicted to be Gram-negative genera, namely Enterobacter, Acinetobacter, Escherichia, and Pseudomonas, pointing out the role of these bacteria as reservoirs of AMR determinants. In this context, the use of de novo assembly has allowed a more holistic AMR detection strategy, while the reads-based approach has enabled the detection of AMR genes from low abundance bacteria, usually undetectable by assembly-based methods. The application of both reads-based and assembly-based approaches, despite being computationally demanding, has facilitated the comprehensive characterization of a food chain resistome, while also allowing the construction of complete metagenome assembled genomes and the investigation of mobile genetic elements. Our findings suggest that milk filters can successfully be used to investigate the resistome of bulk tank milk through the application of the shotgun metagenomic sequencing. In accordance with our results, raw milk can be considered a source of AMR bacteria and genes; this points out the importance of properly informing food business operators about the risk associated with poor hygiene practices in the dairy production environment and consumers of the potential microbial food safety risks derived from raw milk products consumption. Translating these findings as risk assessment outputs heralds the next generation of food safety controls.
Rationale: To describe the diagnostic and treatment approaches of renal abscesses complicated with acute pyelonephritis in children. Patient concerns: Two children presented with fever, vomiting, and ...abdominal pain with no typical manifestations, like frequent urination, urgency, dysuria, hematuria, foam urine, and lumbago. Renal abscess complicating acute pyelonephritis was diagnosed by B-ultrasound and computed tomography enhancement. Moreover, inflammatory markers were elevated significantly, but routine blood and urine cultures were repeatedly negative. The empirical anti-infection therapy had no obvious effect. A pathogenic diagnosis was confirmed in case two, and macro gene detection in blood and urine guided the follow-up treatment. Diagnoses: Both children were diagnosed with acute gastroenteritis on admission, but renal abscess complicating acute pyelonephritis were diagnosed by imaging examination. Interventions: Both children were given anti-infection therapy of third-generation cephalosporin, which had no obvious effect. Routine blood and urine cultures were repeatedly negative. Case one was changed to piperacillin sodium tazobactam. We further carried out blood and urinary metagenomic next-generation sequencing detection for case two. Meanwhile, meropenem and linezolid anti-infection treatment was given. The results showed overlapping infection with Escherichia coli and Enterococcus faecalis . According to the genetic test results, amoxicillin clavulanate potassium combined with nitrofurantoin were prescribed after discharge. Outcomes: Clinical symptoms of the 2 children disappeared, the infection was controlled, and imaging showed that renal abscess complicated with acute pyelonephritis disappeared. Lessons: The clinical spectrum of renal abscess complicating acute pyelonephritis is vague, with no specific manifestations, and can be easily misdiagnosed. B-ultrasound and computed tomography enhancement are helpful in making a definite diagnosis. Moreover, the sensitivity of routine culture is low, and metagenomic next-generation sequencing might be helpful to detect pathogenic microorganisms and guided treatment. Early treatment with broad-spectrum antibiotics might have favorable outcomes.
Although there is growing evidence that micropollutants can be microbially converted in rapid sand filters of drinking water treatment plants (DWTPs), little is known about the biotransformation ...pathways and associated microbial strains in this process. Here, we constructed sand filter columns filled with manganese or quartz sand obtained from full-scale DWTPs to explore the biotransformation of eight micropollutants. Under seven different empty bed contact times (EBCTs), the column experiments showed that caffeine and atenolol were easily removed (up to 92.1% and 97.6%, respectively) with adsorption and microbial biotransformation of the filters. In contrast, the removal of other six micropollutants (i.e., naproxen, carbamazepine, atrazine, trimethoprim, sulfamethoxazole, and sulfadiazine) in the filters were less than 27.1% at shorter EBCTs, but significantly increased at EBCT = 4 h, indicating the dominant role of microbial biotransformation in these micropollutants removal. Integrated analysis of metagenomic reads and transformation products of micropollutants showed a shift in caffeine oxidation and demethylation pathways at different EBCTs, simultaneous occurrence of atrazine hydrolysis and oxidation pathways, and sulfadiazine and sulfamethoxazole oxidation in the filters. Furthermore, using genome-centric analysis, we observed previously unidentified degrading strains, e.g., Piscinibacter, Hydrogenophaga, and Rubrivivax for caffeine transformation, and Methylophilus and Methyloversatilis for atenolol transformation.
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•Microbial transformation of eight micropollutants in sand filters were investigated.•Differential biomass but similar metabolic rates appeared in two types of filters.•Two pathways involved in caffeine and atrazine biotransformation were identified.•Presence of abundant oxygenases hinted the intensive oxidation of micropollutants.•Genome centric analysis revealed unknown micropollutants-degrading bacteria.
Photocatalysis, as a novel technique, has been widely used for antibiotic pollution remediation in wastewater. In the processes of degradation and removal of antibiotics, the impact of photocatalysts ...on microenvironment is very important but remains poorly understood. In the present study, the effect of typical photocatalyst g-C
3
N
4
(Graphitic carbon nitride) on microbial community was investigated in two sediment types (riverbed sediment and pig-farm sediment) polluted by tetracycline (TC) in central southern China. The riverbed sediment and pig farm sediment samples were respectively exposed to g-C
3
N
4
(25, 75, 125 mg⋅kg
–1
) and TC (60, 120, 180 mg⋅L
–1
) treatments alone or combination for 30 days, respectively. The bacterial community and antibiotic resistance genes (ARGs) of the treated sediments were analyzed by Illumina sequencing and metagenomic sequencing. Studies had shown that: TC, g-C
3
N
4
, and TC/g-C
3
N
4
have significant effects on the changes of microbial communities and components in riverbed sediment, but they do not exist in pig farm sediment. The most alterations of microbial taxa were
Acidobacteriota
,
Actinobacteriota
, and
Desulfobacterota
in riverbed sediment, and
Elusimicrobiota
in the pig farm sediment under various treatments. Through network analysis, it was found that the distribution of microorganisms in the pig farm sediment is more complex and more stable. The addition of g-C
3
N
4
reduced the absolute abundance of ARGs in the two examined sediments, but not significantly changed their relative abundance of ARGs. The g-C
3
N
4
application was beneficial to the removal of TC residues and to the prevention of the generation and transmission of ARGs in sediments. Our results suggested that g-C
3
N
4
was a suitable photocatalyst with excellent application prospect for the removal of TC residues and the control of ARGs in environment.
Trace amines (TA) are endogenously produced in mammals, have a low concentration in the central nervous system (CNS), but trigger a variety of neurological effects and intervene in host cell ...communication. It emerged that neurotransmitters and TA are produced also by the microbiota. As it has been shown that TA contribute to wound healing, we examined the skin microbiome of probands using shotgun metagenomics. The phyla Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were predominant. Since SadA is a highly promiscuous TA-producing decarboxylase in Firmicutes, the skin microbiome was specifically examined for the presence of
-homologous genes. By mapping the reads of certain genes, we found that, although there were less reads mapping to
than to ubiquitous housekeeping genes (
and
), normalized reads counts were still >1000 times higher than those of rare control genes (
,
, and
). At protein sequence level SadA homologs were found in at least 7 phyla: Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and Cyanobacteria, and in 23 genera of the phylum Firmicutes. A high proportion of the genera that have a SadA homolog belong to the classical skin and intestinal microbiota. The distribution of
in so many different phyla illustrates the importance of horizontal gene transfer (HGT). We show that the
gene is widely distributed in the human skin microbiome. When comparing the
read counts in the probands, there was no correlation between age and gender, but an enormous difference in the
read counts in the microbiome of the individuals. Since
is involved in TA synthesis, it is likely that the TA content of the skin is correlated with the amount of TA producing bacteria in the microbiome. In this way, the microbiome-generated TA could influence signal transmission in the epithelial and nervous system.
Harmful algal blooms (HABs) are an ecological concern but relatively few studies have investigated the functional potential of bacterioplankton over a complete algal bloom cycle, which is critical ...for determining their contribution to the fate of algal blooms. To address this point, we carried out a time-series metagenomic analysis of the functional features of microbial communities at three different Gymnodinium catenatum bloom stages (pre-, peak-, and post-bloom). Different microbial composition were observed during the blooming stages. The environmental parameters and correlation networks co-contribute to microbial variability, and the former explained 38.4% of total variations of the bacterioplankton community composition. Functionally, a range of pathways involved in carbon, nitrogen, phosphorus and sulfur cycling were significantly different during the various HAB stages. Genes associated with carbohydrate-active enzymes, denitrification, and iron oxidation were enriched at the pre-bloom stage; genes involved in reductive citrate cycle for carbon fixation, carbon degradation, nitrification and phosphate transport were enhanced at the peak stage; and relative gene abundance related to sulfur oxidation, vitamin synthesis, and iron transport and storage was increased at the post-bloom stage. The ecological linkage analysis has shown that microbial functional potential especially the C/P/Fe metabolism were significantly linked to the fate of the algal blooms. Taken together, our results demonstrated that microorganisms displayed successional patterns not only at the community level, but also in the metabolic potential on HAB’s progression. This work contributes to a growing understanding of microbial structural elasticity and functional plasticity and shed light on the potential mechanisms of microbial-mediated HAB trajectory.
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•Environmental parameters and inter-network shape bacterioplankton succession together.•Microbial function involved in C/N/P/S/Fe process significant different over HAB stages.•Microbial structure and related ecophysiological profiles influence HAB trajectory.•There is an ecological linkage between microbial functional potential and HAB formation.
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.
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•RSD decreased soil ARG types and numbers, and changed its composition.•RSD inhibited ARG host genera in Proteobacteria, Actinobacteria and Deinococcus-Thermus.•Bacterial community and soil properties explained most of the ARG composition variance.
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