Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake

Thinning alters nitrogen transformation processes in subtropical forest soil: Key roles of physicochemical properties

Thinning-a widely used forest management practice-can significantly influence soil nitrogen (N) cycling processes in subtropical forests. However, the effects of different thinning intensities on nitrification, denitrification, and their relationships with soil properties and microbial communities remain poorly understood. Here, we conducted a study in a subtropical forest in China and applied three thinning treatments, i.e., no thinning (0 %), intermediate thinning (10-15 %), and heavy thinning (20-25 %), and investigated the effects of thinning intensity on the potential nitrification rate (PNR), potential denitrification rate (PDR), and microbial communities. Moreover, we explored the relationships among soil physicochemical properties, microbial community structure, and nitrogen transformation rates under different thinning intensities. Our results showed that intermediate and heavy thinning significantly increased the PNR by 87 % and 61 % and decreased the PDR by 31 % and 50 % compared to that of the control, respectively. Although the bacterial community structure was markedly influenced by thinning, the fungal community structure remained stable. Importantly, changes in microbial community composition and diversity had minimal impacts on the nitrogen transformation processes, whereas soil physicochemical properties, such as pH, organic carbon content, and nitrogen forms, were identified as the primary drivers. These findings highlight the critical role of managing soil physicochemical properties to regulate nitrogen transformations in forest soils. Effective forest management should focus on precisely adjusting the thinning intensity to enhance the soil physicochemical conditions, thereby promoting more efficient nitrogen cycling and improving forest ecosystem health in subtropical regions.

How do glyphosate and AMPA alter the microbial community structure and phosphorus cycle in rice-crayfish systems?

Glyphosate, a commonly used organophosphorus herbicide in rice-crayfish cropping regions, may alter regional phosphorus cycle processes while affecting the structure of microbial communities. However, the effects of glyphosate residues on rice-crayfish systems remain unclear. In this study, we assessed the spatial and temporal distribution characteristics of glyphosate and its primary degradation products, as well as the impact mechanisms of glyphosate on microbial communities and the phosphorus cycle in rice-crayfish systems such as paddy fields, breeding ditches and recharge rivers. The detection rates of glyphosate and aminomethylphosphonic acid (AMPA) were 100% in rice-crayfish systems. Concentrations of glyphosate in the water phase and soil/sediment were as high as 0.012 μg/L and 7.480 μg/kg, respectively, and concentrations of AMPA were as high as 17.435 μg/L and 13.200 μg/kg, respectively. Glyphosate concentrations were not affected by rainfall or sampling site, but concentrations of AMPA in the water phase of recharge rivers were affected by rainfall. The glyphosate concentration was significantly and positively correlated with RBG-16-58-14 abundance, and the AMPA concentration was significantly and positively correlated with Actinobacteria and Lysobacter abundance, and negatively correlated with Cyanobacteria abundance (P < 0.05). The highest abundances of phoD, phnK, and ppx genes were found in all soils/sediments. Glyphosate concentration in soil/sediment was significantly and positively correlated with the abundance of phoD gene encoding an organophosphorus-degrading enzyme and ppx gene encoding poly inorganic phosphate (Pi) hydrolase (P < 0.05). In addition, the glyphosate concentration was significantly and positively correlated with the Ca-bonded Pi content (P < 0.05). This implies that glyphosate may promote the production of stable Pi in rice-crayfish systems by increasing the abundance of phoD and ppx genes. The results of this study reveal the impact mechanism of glyphosate on the phosphorus cycle in rice-crayfish systems and provide a basis for the risk assessment of glyphosate.

Characterization of dry-cured ham microbiota at 12 months of seasoning obtained from different rearing strategies using 16S rRNA profiling

In this study, we investigated the microbiota of 72 Italian ham samples collected after 12 months of seasoning. The hams were elaborated from pigs fed different rearing methods, including the traditional restricted medium protein diet chosen as control (C group); restrictive low protein diet (LP group); two ad libitum high-protein diet groups (HP9M group: slaughter at 9 months of age; HP170 group: slaughter at 170 kg). A multi-amplicon 16S metabarcoding approach was used, and a total of 2845 Amplicon Sequence Variants were obtained from the 72 ham samples. Main phyla included: Firmicutes (90.8%), Actinobacteria (6.2%), Proteobacteria (2.7%), and Bacteroidota (0.12%). The most common genera were Staphylococcus, Tetragenococcus, and Brevibacterium. Shannon index for α-diversity was found statistically significant, notably for the HP9M group, indicating higher diversity compared to C. PERMANOVA test on β-diversity showed significant differences in rearing methods between HP170 and C, HP170 and LP, and HP9M vs. C. All three rearing methods revealed associations with characteristic communities: the HP9M group had the highest number of associations, many of which were due to spoilage bacteria, whereas the LP group had the highest number of seasoning-favourable genera.

Assembly mechanism of microbial community under different seasons in Shantou sea area

Coastal areas are often affected by a variety of climates, and microbial composition patterns are conducive to adaptation to these environments. In this study, the composition and pattern of microbial communities in the Shantou sea from four seasons were analyzed. The diversity of microbial community was significant differences under different seasons (p < 0.01). Meanwhile, dissolved oxygen levels, temperature were key factors to shift microbial communities. The assembly mechanism of microbial communities was constructed by the iCAMP (Infer community assembly mechanism by the phylogenetic bin-based null). Interestingly, the analyses revealed that drift was the predominant driver of this process (44.5 %), suggesting that microbial community assembly in this setting was dominated by stochastic processes. For example, Vibrio was found to be particularly susceptible to stochastic processes, indicating that the pattern of bacterial community was governed by stochastic processes. Thus, these results offering novel insight into the regulation of microbial ecology in marine environments.

Biocontrol and growth promotion potential of Bacillus velezensis NT35 on Panax ginseng based on the multifunctional effect

The Bacillus velezensis strain NT35, which has strong biocontrol ability, was isolated from the rhizosphere soil of Panax ginseng. The antifungal effects of the NT35 strain against the mycelium and spore growth of Ilyonectria robusta, which causes ginseng rusty root rot, were determined. The inhibitory rate of I. robusta mycelial growth was 94.12% when the concentration of the NT35 strain was 107 CFU·mL-1, and the inhibitory rates of I. robusta sporulation and spore germination reached 100 and 90.31%, respectively, when the concentration of the NT35 strain was 104 and 108 CFU·mL-1, respectively. Strain NT35 had good prevention effects against ginseng rust rot indoors and in the field with the control effect 51.99%, which was similar to that of commercial chemical and biocontrol agents. The labeled strain NT35-Rif160-Stre400 was obtained and colonized ginseng roots, leaves, stems and rhizosphere soil after 90 days. Bacillus velezensis NT35 can induce a significant increase in the expression of five defensive enzyme-encoding genes and ginsenoside biosynthesis-related genes in ginseng. In the rhizosphere soil, the four soil enzymes and the microbial community improved during different periods of ginseng growth in response to the biocontrol strain NT35. The NT35 strain can recruit several beneficial bacteria, such as Luteimonas, Nocardioides, Sphingomonas, and Gemmatimonas, from the rhizosphere soil and reduce the relative abundance of Ilyonectria, Fusarium, Neonectria and Dactylonectria, which cause root rot and rusty root rot in ginseng plants. The disease indices were significantly negatively correlated with the abundances of Sphingomonas and Trichoderma. Additionally, Sphingomonadales, Sphingomonadaceae and actinomycetes were significantly enriched under the NT35 treatment according to LEfSe analysis. These results lay the foundation for the development of a biological agent based on strain NT35.

Comparative evaluation of 16S rRNA primer pairs in identifying nitrifying guilds in soils under long-term organic fertilization and water management

Compared with 454 sequencing technology, short-read sequencing (e.g., Illumina) technology generates sequences of high accuracy, but limited length (<500 bp). Such a limitation can prove that studying a target gene using a large amplicon (>500 bp) is challenging. The ammonia monooxygenase subunit A (amoA) gene of ammonia-oxidizing archaea (AOA), which plays a crucial part in the nitrification process, is such a gene. By providing a full overview of the community of a functional microbial guild, 16S ribosomal ribonucleic acid (rRNA) gene sequencing could overcome this problem. However, it remains unclear how 16S rRNA primer selection influences the quantification of relative abundance and the identification of community composition of nitrifiers, especially AOA. In the present study, a comparison was made between the performance of primer pairs 338F-806R, 515F-806R, and 515F-907R to a shotgun metagenome approach. The structure of nitrifier communities subjected to different long-term organic matter amendment and water management protocols was assessed. Overall, we observed higher Chao1 richness diversity of soil total bacteria by using 515F-806R compared to 338F-806R and 515F-907R, while higher Pielou's evenness diversity was observed by using 515F-806R and 515F-907R compared to 338F-806R. The studied primer pairs revealed different performances on the relative abundance of Thaumarchaeota, AOB, and NOB. The Thaumarchaeota 16S rRNA sequence was rarely detected using 338F-806R, while the relative abundances of Thaumarchaeota detected using 515F-806R were higher than those detected by using 515F-907R. AOB showed higher proportions in the 338F-806R and 515F-907R data, than in 515F-806R data. Different primers pairs showed significant change in relative proportion of NOB. Nonetheless, we found consistent patterns of the phylotype distribution of nitrifiers in different treatments. Nitrosopumilales (NP) and Nitrososphaerales (NS) clades were the dominant members of the AOA community in soils subject to controlled irrigation, whereas Ca. Nitrosotaleales (NT) and NS clades dominated the AOA community in soils subject to flooding irrigation. Nitrospira lineage II was the dominant NOB phylotype in all samples. Overall, ideal 16S rRNA primer pairs were identified for the analysis of nitrifier communities. Moreover, NP and NT clades of AOA might have distinct environmental adaptation strategies under different irrigation treatments.

Detection of Mtb and NTM: preclinical validation of a new asymmetric PCR-binary deoxyribozyme sensor assay

Tuberculosis (TB) and infectious diseases caused by non-tuberculous mycobacteria (NTM) are global concerns. The development of a rapid and accurate diagnostic method, capable of detecting and identifying different mycobacteria species, is crucial. We propose a molecular approach, the BiDz-TB/NTM, based on the use of binary deoxyribozyme (BiDz) sensors for the detection of Mycobacterium tuberculosis (Mtb) and NTM of clinical interest. A panel of DNA samples was used to evaluate Mtb-BiDz, Mycobacterium abscessus/Mycobacterium chelonae-BiDz, Mycobacterium avium-BiDz, Mycobacterium intracellulare/Mycobacterium chimaera-BiDz, and Mycobacterium kansasii-BiDz sensors in terms of specificity, sensitivity, accuracy, and limit of detection. The BiDz sensors were designed to hybridize specifically with the genetic signatures of the target species. To obtain the BiDz sensor targets, amplification of a fragment containing the hypervariable region 2 of the 16S rRNA was performed, under asymmetric PCR conditions using the reverse primer designed based on linear-after-the-exponential principles. The BiDz-TB/NTM was able to correctly identify 99.6% of the samples, with 100% sensitivity and 0.99 accuracy. The individual values of specificity, sensitivity, and accuracy, obtained for each BiDz sensor, satisfied the recommendations for new diagnostic methods, with sensitivity of 100%, specificity and accuracy ranging from 98% to 100% and from 0.98 to 1.0, respectively. The limit of detection of BiDz sensors ranged from 12 genome copies (Mtb-BiDz) to 2,110 genome copies (Mkan-BiDz). The BiDz-TB/NTM platform would be able to generate results rapidly, allowing the implementation of the appropriate therapeutic regimen and, consequently, the reduction of morbidity and mortality of patients.IMPORTANCEThis article describes the development and evaluation of a new molecular platform for accurate, sensitive, and specific detection and identification of Mycobacterium tuberculosis and other mycobacteria of clinical importance. Based on BiDz sensor technology, this assay prototype is amenable to implementation at the point of care. Our data demonstrate the feasibility of combining the species specificity of BiDz sensors with the sensitivity afforded by asymmetric PCR amplification of target sequences. Preclinical validation of this assay on a large panel of clinical samples supports the further development of this diagnostic tool for the molecular detection of pathogenic mycobacteria.

Unlocking the potential of bacterioplankton-mediated microcystin degradation and removal: A bibliometric analysis of sustainable water treatment strategies

Microcystins (MCs) constitute a significant threat to human and environmental health, urging the development of effective removal methods for these toxins. In this review, we explore the potential of MC-degrading bacteria as a solution for the removal of MCs from water. The review insights into the mechanisms of action employed by these bacteria, elucidating their ability to degrade and thus remove MCs. After, the review points out the influence of the structural conformation of MCs on their removal, particularly their stability at different water depths within different water bodies. Then, we review the crucial role played by the production of MCs in ensuring the survival and safeguarding of the enzymatic activities of Microcystis cells. This justifies the need for developing effective and sustainable methods for removing MCs from aquatic ecosystems, given their critical ecological function and potential toxicity to humans and animals. Thereafter, challenges and limitations associated with using MC-degrading bacteria in water treatment are discussed, emphasizing the need for further research to optimize the selection of bacterial strains used for MCs biodegradation. The interaction of MCs-degrading bacteria with sediment particles is also crucial for their toxin removal potential and its efficiency. By presenting critical information, this review is a valuable resource for researchers, policymakers, and stakeholders involved in developing sustainable and practical approaches to remove MCs. Our review highlights the potential of various applications of MC-degrading bacteria, including multi-soil-layering (MSL) technologies. It emphasizes the need for ongoing research to optimize the utilization of MC-degrading bacteria in water treatment, ultimately ensuring the safety and quality of water sources. Moreover, this review highlights the value of bibliometric analyses in revealing research gaps and trends, providing detailed insights for further investigations. Specifically, we discuss the importance of employing advanced genomics, especially combining various OMICS approaches to identify and optimize the potential of MCs-degrading bacteria.

Uncovering the microbial diversity of Czech Republic archives: A study of metabolically active airborne microbes

Despite the diligent efforts of libraries, archives, and similar institutions to preserve cultural monuments, biodeterioration continues to pose a significant threat to these objects. One of the main sources of microorganisms responsible for the biodeterioration process is the presence of airborne microorganisms. Therefore, this research aims to monitor and compare outcomes of both culture-dependent (utilising various cultivation strategies) and culture-independent approaches (RNA-based sequencing) to identifying metabolically active airborne microorganisms in archives in the Czech Republic. Through this study, several species that have the potential to pose risks to both cultural heritage objects and the health of institution employees were found. Additionally, the efficacy of different cultivation media was demonstrated to be varied across archive rooms, highlighting the necessity of employing multiple cultivation media for comprehensive analyses. Of noteworthy importance, the resuscitating-promoting factor (Rpf) proved to be a pivotal tool, increasing bacterial culturability by up to 30% when synergistically employed Reasoner's 2A agar (R2A) and R2A + Rpf media. Next, the study emphasises the importance of integrating both culture-dependent and culture-independent approaches. The overlap between genera identified by the culture-dependent approach and those identified also by the culture-independent approach varied from 33% to surpassing 94%, with the maximum alignment exceeding 94% in only one case. Our results highlight the importance of actively monitoring and assessing levels of microbial air contamination in archives to prevent further deterioration of cultural heritage objects and to promote improved conditions for employees in archives and similar institutions.

Survival of an Antarctic cyanobacterial mat under Martian conditions

Antarctica is one of the most outstanding analogs of Mars, and cyanobacterial mats are considered one of the most resilient biological consortia. The purpose of this study is to find out the effect of the Martian conditions on an Antarctic cyanobacterial mat. We exposed an Antarctic microbial mat to Martian conditions in a simulating chamber (MARTE) for 15 d and investigated the variations in the consortium by the use of 16S rRNA gene expression as an indicator of the biological activity. Metabarcoding using the V3-V4 regions of the 16S rRNA gene was used to determine the succession of the active members of the microbial consortium during the experiment. The results showed that the microbial mat, far from collapsing, can survive the stringent conditions in the simulating chamber. Different behaviors were displayed depending on the metabolic capabilities and physiological characteristics of every taxon. The main conclusion is that the Martian conditions did not impair growth in some of the groups, and thus, the investigated Antarctic community would be able to survive in a Martian environment at least during the short experimental period, although elements of the community were affected in different ways.

Eutrophication increases the similarity of cyanobacterial community features in lakes and reservoirs

Eutrophication of inland waters is a mostly anthropogenic phenomenon impacting aquatic biodiversity worldwide, and might change biotic community structure and ecosystem functions. However, little is known about the patterns of cyanobacterial community variations and changes both on alpha and beta diversity levels in response to eutrophication. Here, we investigated cyanobacterial communities sampled at 140 sites from 59 lakes and reservoirs along a strong eutrophication gradient in eastern China through using CPC-IGS and 16S rRNA gene amplicon sequencing. We found that taxonomic diversity increased, but phylogenetic diversity decreased significantly along the eutrophication gradient. Both niche width and niche overlap of cyanobacteria significantly decreased from low- to high-nutrient waterbodies. Cyanobacterial community distance-decay relationship became weaker from mesotrophic to hypereutrophic waterbodies, while ecological uniqueness (i.e., local contributions to beta diversity) tended to increase in high-nutrient waterbodies. Latitude and longitude were more important in shaping cyanobacterial community structure than other environmental variables. These findings suggest that eutrophication affects alpha and beta diversity of cyanobacterial communities, leading to increasingly similar community structures in lakes and reservoirs with a higher level of eutrophication. Our work highlights how cyanobacterial communities respond to anthropogenic eutrophication and calls for an urgent need to develop conservation and management strategies to control lake eutrophication and protect freshwater biodiversity.

Quantitative real-time PCR and magnetic separation strategy for specific detection of group B streptococcus in perinatal Women's urine

Introduction

Group B streptococcus(GBS)often causes adverse outcomes such as urinary system infection, intrauterine infection, premature birth, and stillbirth in perinatal women. Perinatal screening of GBS is conducive to guiding clinical scientific intervention and improving delivery outcomes.This study quantitative real-time PCR (RT-qPCR) combined with magnetic separation was used for GBS detection.

Materials and methods

Sample pre-treatment in this study involved the utilization of magnetic separation (MS) technology, aiming to expedite the detection process and enhance detection sensitivity, and the cfb gene of group B streptococcus was used as the target gene to establish quantitative real-time PCR (RT-qPCR) to detect group B streptococcus.

Results

It was found that penicillin-functionalized magnetic beads had a good ability to enrich and capture group B Streptococcus.The findings revealed an exceptional detection sensitivity, with the ability to detect B streptococcus in urine samples at levels as low as 102 CFU/mL.

Conclusions

The utilization of MS technology in conjunction with the RT-qPCR (MS-RT-qPCR) assay, as demonstrated in this study, offers a viable approach for prenatal screening of group B streptococcus among perinatal women.

Stabilization of Ni by rhamnolipid modified nano zero-valent iron in soil: Effect of simulated acid rain and microbial response

Nickel (Ni), as one of the essential micronutrients, exists widely in nature, but high concentration of Ni in soil can pose certain biological toxicity. Nano zero-valent iron (nZVI) and rhamnolipid modified nZVI (RL@nZVI) can effectively stabilize Ni in soil. In this study, the stabilization effect of nZVI and RL@nZVI on the Ni-polluted soil under simulated acid rain and the microbial community response during the soil remediation under different Ni levels (200, 600, and 1800 mg/kg) were investigated. The results show that the addition of nZVI and RL@nZVI increased the pH of leachate to neutral and decreased the amount of Ni in leachate (23.33%-47.06% by nZVI and 50.01%-70.47% by RL@nZVI), indicating that nZVI and RL@nZVI could reduce the potential radial migration risk of Ni in soil under simulated acid rain. The addition of RL@nZVI was beneficial to recover the soil bacterial community diversity, which was inhibited by Ni pollution, and rhamnolipid coating could reduce the toxicity of nZVI. The dominant bacteria in RL@nZVI-treated soil with low, medium, and high Ni pollution were Firmicutes, Proteobacteria and Actinobacteria, respectively. Soil potential, total organic carbon, and pH were the main driving factors affecting the bacterial community structure, while Ni stress only caused changes in the relative abundance of some tolerant bacteria.

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene-derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome-based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome-specific methods for accounting for or correcting them.

Bacterial Communities of the Internal Reproductive and Digestive Tracts of Virgin and Mated Tuta absoluta

Microorganisms can affect host reproduction, defense, and immunity through sexual or opportunistic transmission; however, there are few studies on insect reproductive organs and intestinal bacterial communities and their effects on mating. Tuta absoluta is a worldwide quarantine pest that seriously threatens the production of Solanaceae crops, and the microbial community within tomato leafminers remains unclear. In this study, 16s rRNA sequencing was used to analyze bacterial communities related to the reproductive organs and intestinal tracts of tomato leafminers (the sample accession numbers are from CNS0856533 to CNS0856577). Different bacterial communities were found in the reproductive organs and intestinal tracts of females and males. Community ecological analysis revealed three potential signs of bacterial sexual transmission: (1) Mating increased the similarity between male and female sex organs and intestinal communities. (2) The bacteria carried by mated individuals were found in unmated individuals of the opposite sex but not in unmated individuals of the same sex. (3) The bacteria carried by unmated individuals were lost after mating. In addition, the abundances of bacterial communities carried by eggs were significantly higher than those of adult worms. Our results confirm that mating leads to the transfer of bacterial communities in the reproductive organs and gut of tomato leafminers, and suggest that this community strongly influences the reproductive process.

Evaluation of different 16S rRNA gene hypervariable regions and reference databases for profiling engineered microbiota structure and functional guilds in a swine wastewater treatment plant

High-throughput 16S rRNA gene amplicon sequencing technology is widely applied for environmental microbiota structure analysis to derive knowledge that informs microbiome-based surveillance and oriented bioengineering. However, it remains elusive how the selection of 16S rRNA gene hypervariable regions and reference databases affects microbiota diversity and structure profiling. This study systematically evaluated the fitness of different frequently used reference databases (i.e. SILVA 138 SSU, GTDB bact120_r207, Greengenes 13_5 and MiDAS 4.8) and primers of 16S rRNA gene in microbiota profiling of anaerobic digestion and activated sludge collected from a full-scale swine wastewater treatment plant (WWTP). The comparative results showed that MiDAS 4.8 achieved the highest levels of taxonomic diversity and species-level assignment rate. For whichever sample groups, microbiota richness captured by different primers decreased in the following order: V4 > V4-V5 > V3-V4 > V6-V8/V1-V3. Using primer-bias-free metagenomic data results as the judging standard, V4 region also best characterized microbiota structure and well represented typical functional guilds (e.g. methanogens, ammonium oxidizers and denitrifiers), while V6-V8 regions largely overestimated the archaeal methanogens (mainly Methanosarcina) by over 30 times. Therefore, MiDAS 4.8 database and V4 region are recommended for best simultaneous analysis of bacterial and archaeal community diversity and structure of the examined swine WWTP.

Gut Microbial Alteration in MPTP Mouse Model of Parkinson Disease is Administration Regimen Dependent

Parkinson Disease (PD) is one of the most common neurodegenerative disorders characterized by loss of dopaminergic neurons involved in motor functions. Growing evidence indicates that gut microbiota communicates with the brain known as the gut-brain axis (GBA). Mitochondrial toxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is commonly used in animal studies to investigate the GBA in PD. Various MPTP administration regimens are performed in PD mouse models involving one to multiple injections in 1 day or one injection per day for several days. The aim of this study is to investigate if the impact of MPTP on gut microbiota differs depending on the administration regimen. C57BL/6 mice were treated with acute or subchronic regimens of MPTP. Motor functions were assessed by open-field, catalepsy, and wire hanging tests. The cecum and the brain samples were obtained for microbiota and gene expression analyses, respectively. MPTP administration regimens differed in their ability to alter the gut microbiota. Firmicutes and Bacteroidota were both increased in subchronic mice while did not change and decreased, respectively, in acute mice. Verrucomicrobiota was elevated in acute MPTP mice but dropped in subchronic MPTP mice. Muribaculaceae was the predominant genus in all groups but acute mice. In acute mice, Akkermansia was increased and Colidextribacter was decreased; however, they showed an opposite trend in subchronic mice. These data suggest that MPTP mouse model cause a gut microbiota dysbiosis in an administration regimen dependent manner, and it is important to take consideration of mouse model to investigate the GBA in neurodegenerative diseases including PD.

Field investigation on the change process of microbial community structure in large-deep reservoir during the initial impoundment

During the initial impoundment of large-deep reservoir, the aquatic environment changed dramatically in various aspects such as water level, hydrological regime, and pollutants, which could alter microorganisms' community structure, break the balance of the aquatic ecosystem and even endanger the aquatic ecosystem. However, the interaction of microbial communities and water environment during the initial impoundment process of a large-deep reservoir remained unclear. To this end, in-situ monitoring and sampling analysis on water quality and microbial communities during the initial impoundment process of a typical large-deep reservoir named Baihetan were conducted so as to explore the response of microbial community structure to the changes of water environmental factors during the initial impoundment of large deep reservoir and reveal the key driving factors affecting microbial community structure. The spatio-temporal variation in water quality was analyzed, and the microbial community structure in the reservoir was investigated based on high-throughput sequencing. The results showed that the COD of each section increased slightly, and the water quality after impoundment was slightly poorer than that before the impoundment. Water temperature and pH were proved to be the key factors affecting the structure of bacterial and eukaryotic communities respectively during the initial impoundment. The research results revealed the role of microorganisms and their interaction with biogeochemical processes in the large-deep reservoir ecosystem, which was crucial for later operation and management of the reservoir and the protection of the reservoir water environment.

Pollutant impacts on bacteria in surface water and sediment: Conventional versus emerging pollutants in Taihu Lake, China

Bacteria play a critical role in biogeochemical cycling, self-purification, and food web fueling in surface freshwater ecosystems. However, the comparison between the impacts of conventional and emerging pollutants on the bacteria in surface water and sediment remains unclear and requires for an in-depth understanding to assess ecological risk and select associated bioindicators. Taihu Lake, a typical shallow lake in China, was divided into pollutant impacted and less-impacted zones for sampling. Spatial distributions of conventional pollutants, emerging pharmaceuticals, and bacterial communities were investigated in surface water and sediment. The correlations of pollutants with bacterial communities and the variations in bacterial functions were analyzed to help assess the pollutant influences on bacteria. The results showed that the water quality index and trophic level index across the whole lake were at medium to good, and mesotropher to light eutropher grades, respectively, indicating a relatively good control on conventional pollutants in water. Target pharmaceuticals were at much higher concentrations in water of the impacted zone compared to the less-impacted zone, exhibiting close positive relationships with the bacterial phyla in the impacted water. The ratio of Firmicutes to Proteobacteria in surface water is suggested as a plausible bioindicator to evaluate the level of inflow pharmaceutical contamination and the risk of relevant bacterial resistance in the outflow. In sediment, no significant difference was observed for pharmaceuticals between the two zones, whereas total phosphorus and orthophosphate were substantially higher in the impacted zone. Phosphorus pollutants were tightly associated with the bacterial genera in the impacted sediment, likely relating to the increase in iron- or sulfate-reducing bacteria which implies the potential risk of phosphorus releasing from sediment to water.

In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea

BACKGROUND

Sequencing has been widely used to study the composition of the oral microbiome present in various health conditions. The extent of the coverage of the 16S rRNA gene primers employed for this purpose has not, however, been evaluated in silico using oral-specific databases. This paper analyses these primers using two databases containing 16S rRNA sequences from bacteria and archaea found in the human mouth and describes some of the best primers for each domain.

RESULTS

A total of 369 distinct individual primers were identified from sequencing studies of the oral microbiome and other ecosystems. These were evaluated against a database reported in the literature of 16S rRNA sequences obtained from oral bacteria, which was modified by our group, and a self-created oral archaea database. Both databases contained the genomic variants detected for each included species. Primers were evaluated at the variant and species levels, and those with a species coverage (SC) ≥75.00% were selected for the pair analyses. All possible combinations of the forward and reverse primers were identified, with the resulting 4638 primer pairs also evaluated using the two databases. The best bacteria-specific pairs targeted the 3-4, 4-7, and 3-7 16S rRNA gene regions, with SC levels of 98.83-97.14%; meanwhile, the optimum archaea-specific primer pairs amplified regions 5-6, 3-6, and 3-6, with SC estimates of 95.88%. Finally, the best pairs for detecting both domains targeted regions 4-5, 3-5, and 5-9, and produced SC values of 95.71-94.54% and 99.48-96.91% for bacteria and archaea, respectively.

CONCLUSIONS

Given the three amplicon length categories (100-300, 301-600, and >600 base pairs), the primer pairs with the best coverage values for detecting oral bacteria were as follows: KP_F048-OP_R043 (region 3-4; primer pair position for Escherichia coli J01859.1: 342-529), KP_F051-OP_R030 (4-7; 514-1079), and KP_F048-OP_R030 (3-7; 342-1079). For detecting oral archaea, these were as follows: OP_F066-KP_R013 (5-6; 784-undefined), KP_F020-KP_R013 (3-6; 518-undefined), and OP_F114-KP_R013 (3-6; 340-undefined). Lastly, for detecting both domains jointly they were KP_F020-KP_R032 (4-5; 518-801), OP_F114-KP_R031 (3-5; 340-801), and OP_F066-OP_R121 (5-9; 784-1405). The primer pairs with the best coverage identified herein are not among those described most widely in the oral microbiome literature. Video Abstract.

Impact of 16S rRNA Gene Redundancy and Primer Pair Selection on the Quantification and Classification of Oral Microbiota in Next-Generation Sequencing

This study aimed to evaluate the number of 16S rRNA genes in the complete genomes of the bacterial and archaeal species inhabiting the human mouth and to assess how the use of different primer pairs would affect the detection and classification of redundant amplicons and matching amplicons (MAs) from different taxa. A total of 518 oral-bacterial and 191 oral-archaeal complete genomes were downloaded from the NCBI database, and their complete 16S rRNA genes were extracted. The numbers of genes and variants per genome were calculated. Next, 39 primer pairs were used to search for matches in the genomes and obtain amplicons. For each primer, we calculated the number of gene amplicons, variants, genomes, and species detected and the percentage of coverage at the species level with no MAs (SC-NMA). The results showed that 94.09% of oral bacteria and 52.59% of oral archaea had more than one intragenomic 16S rRNA gene. From 1.29% to 46.70% of bacterial species and from 4.65% to 38.89% of archaea detected by the primers had MAs. The best primers were the following (SC-NMA; region; position for Escherichia coli [GenBank version no. J01859.1]): KP_F048-OP_R030 for bacteria (93.55%; V3 to V7; 342 to 1079), KP_F018-KP_R063 for archaea (89.63%; V3 to V9; undefined to 1506), and OP_F114-OP_R121 for both domains (92.52%; V3 to V9; 340 to 1405). In addition to 16S rRNA gene redundancy, the presence of MAs must be controlled to ensure an accurate interpretation of microbial diversity data. The SC-NMA is a more useful parameter than the conventional coverage percentage for selecting the best primer pairs. The pairs used the most in the oral microbiome literature were not among the best performers. IMPORTANCE Hundreds of publications have studied the oral microbiome through 16S rRNA gene sequencing. However, none have assessed the number of 16S rRNA genes in the genomes of oral microbes, or how the use of primer pairs targeting different regions affects the detection of MAs from different taxa. Here, we found that almost all oral bacteria and more than half of oral archaea have more than one intragenomic 16S rRNA gene. The performance of the primer pairs in not detecting MAs increases as the length of the amplicon augments. As none of those most employed in the oral literature were among the best performers, we selected a series of primers to detect bacteria and/or archaea based on their percentage of species detected without MAs. The intragenomic 16S rRNA gene redundancy and the presence of MAs between distinct taxa need to be considered to ensure an accurate interpretation of microbial diversity data.

Biochar combined with Bacillus subtilis SL-44 as an eco-friendly strategy to improve soil fertility, reduce Fusarium wilt, and promote radish growth

Bacillus subtilis as microbial fertilizers contribute to avoiding the harmful effects of traditional agricultural fertilizers and pesticides. However, there are many restrictions on the practical application of fertilizers. In this study, microbial biochar formulations (BCMs) were prepared by loading biochar with B. subtilis SL-44. Pot experiments were conducted to evaluate the effects of the BCMs on soil fertility, Fusarium wilt control, and radish plant growth. The application of BCMs dramatically improved soil properties and favored plant growth. Compared with SL-44 and biochar treatments, the BCMs treatments increased radish plant physical-chemical properties and activities of several enzymes in the soil. What's more, Fusarium wilt incidence had decreased by 59.88%. In addition, the BCMs treatments exhibited a significant increase in the abundance of bacterial genera in the rhizosphere soil of radish. Therefore, this study demonstrated that BCMs may be an eco-friendly strategy for improving soil fertility, reducing Fusarium wilt, and promoting radish plant growth.

Relation Between Dietary Protein Intake and Gut Microbiome Composition in Community-Dwelling Older Men: Findings from the Osteoporotic Fractures in Men Study (MrOS)

BACKGROUND

Little is known about the association of specific nutrients, especially proteins, on age-related gut dysbiosis.

OBJECTIVES

To determine the associations between the quantity and sources (vegetable and animal) of dietary protein intake and gut microbiome composition in community-dwelling older men.

METHODS

We performed a cross-sectional analysis on 775 older men from the Osteoporotic Fractures in Men Study (MrOS) (age 84.2 ± 4.0 y) with available dietary information and stool samples at visit 4 (2014-2016). Protein intake was estimated from a brief FFQ and adjusted to total energy intake. The gut microbiome composition was determined by 16S (v4) sequencing (processed by DADA2 and SILVA). A total of 11,534 amplicon sequence variants (ASVs) were identified and assigned to 21 phyla with dominance of Firmicutes (45%) and Bacteroidetes (43%). We performed α-diversity, β-diversity, and taxa abundance (by Analysis of Compositions of Microbiomes with Bias Correction [ANCOM-BC]) to determine the associations between protein intake and the gut microbiome.

RESULTS

Median protein intake was 0.7 g/(kg body weight · d). Participants with higher energy-adjusted protein intakes had higher Shannon and Chao1 α-diversity indices (P < 0.05). For β-diversity analysis, participants with higher protein intakes had a different center in weighted and unweighted UniFrac Principal Co-ordinates Analysis (PCoA) compared with those with lower intake (P < 0.05), adjusted for age, race, education, clinical center, batch number, fiber and energy intake, weight, height, and medications. Similarly, higher protein consumptions from either animal or vegetable sources were associated with higher gut microbiome diversity. Several genus-level ASVs, including Christensenellaceae, Veillonella, Haemophilus, and Klebsiella were more abundant in participants with higher protein intakes, whereas Clostridiales bacterium DTU089 and Desulfovibrio were more abundant in participants with lower protein intake (Bonferroni corrected P < 0.05).

CONCLUSIONS

We observed significant associations between protein intake and gut microbiome diversity in community-living older men. Further studies are needed to elucidate the mediation role of the gut microbiome on the relation between protein intake and health outcomes in older adults.

Bacterial Community Composition and Function of Tropical River Ecosystem along the Nandu River on Hainan Island, China

Microorganisms play a pivotal role in nutrient cycling in aquatic ecosystems. Understanding bacterial diversity and its functional composition are crucial for aquatic ecology and protection. We investigated the bacterial community structure using 16S rRNA gene amplicons high-throughput sequencing in this study. Results showed that 105 amplicon sequence variants (ASVs) account for 43.8% of the total sequences shared by the Nandu River's lower, middle, and upper reach and the Songtao Reservoir. The dominant bacterial phylum in the Nandu River and its connected Songtao Reservoir were Proteobacteria and Actinobacteriota, respectively. The highest Chao1 and Shannon index values were found in the lower reach of the Nandu River. Beta diversity analysis showed the divergence in bacterial communities in the Nandu River and Songtao Reservoir, but not in different reaches. Among the water properties, based on the Mantel test, dissolved oxygen, total nitrogen, and nitrite significantly affected the bacterial communities. The functional profiles predicted by Tax4Fun2 showed that metabolism was the most abundant function group. The relative abundance of genetic information processing was significantly higher in the Songtao Reservoir than in the Nandu River, while the relative abundance of human diseases was significantly lower in the Songtao Reservoir than in the Nandu River. The appearance of the xenobiotics biodegradation and metabolism function group requires us to pay more attention to possible water pollution, especially at the upper reach of the Nandu River.

Comparison of soil microbial community structure and function for karst tiankeng with different degrees of degradation

Karst tiankengs are oases in degraded karst landscapes and act as repositories for biodiversity conservation; however, knowledge about the bacterial and fungal structure and function of the karst tiankeng ecosystems is limited. This study investigated the microbial communities in three different tiankeng (nondegraded, moderately degraded, and heavily degraded tiankeng) by Illumina NovaSeq sequencing. We found that the degradation of karst tiankeng can lead to changes in microbial community structure and functions, while there are differences in bacterial and fungal responses. There were significant differences in bacterial and fungal community composition and beta diversity in the three tiankeng soils. Random molecular ecological network analysis results indicated that a more complex and stable bacterial network existed in nondegraded tiankeng, while more complex fungal networks existed in moderately degraded tiankeng. The keystones of Proteobacteria, Actinobacteria, Acidobacteria, Ascomycota, and Basidiomycota played essential roles in maintaining soil function and stability. The functional profiles revealed that tiankeng habitat changes may affect microbial survival strategies, such as increasing gene abundance associated with the carbon cycle. To our knowledge, this is the first report on bacterial and fungal communities in different degrees of karst tiankeng, which provides crucial insights into our understanding of the microbial communities' structure and potential function in karst tiankeng ecosystems.

Stagnation trigger changes to tap water quality in winter season: Novel insights into bacterial community activity and composition

The drinking water distribution system is important for water supply and it affects the quality of the drinking water. Indoor pipeline water quality is regulated by physical, hydraulic and biological elements, such as indoor temperature and stagnation. In this work, the effects of indoor heating and overnight stagnation on the variation in bacterial community structure and the total cell count were assessed by full-length 16S rRNA gene sequencing and flow cytometry, respectively. The results exhibited that the average intact cell count was 6.99 × 10⁴ cells/mL and the low nucleic acid (LNA) bacteria was 4.48 × 10⁴ cells/mL after stagnation. The average concentration of total and intracellular adenosine triphosphate (ATP) was 3.64 × 10^-12 gATP/mL and 3.13 × 10^-17 gATP/cell in stagnant water, respectively. The growth of LNA cells played a crucial role in increasing ATP. The dominant phylum observed was Proteobacteria (87.21 %), followed by Actinobacteria (8.25 %). Opportunistic pathogens increased the risk of disease in stagnant water (up to 1.2-fold for Pseudomonas sp. and 5.8-fold for Mycobacterium sp.). Meanwhile, structural equation model (SEM) and redundancy analysis (RDA) also illustrated that water temperature, residual chlorine and Fe significantly affected the abundance and composition of bacterial community. Taking together, these results show response of tap water quality to overnight stagnation and indoor heating, and provide scientific basis for drinking water security management in winter season.

Effects of Early Antiretroviral Therapy on the Composition and Diversity of the Fecal Microbiome of SIV-infected Rhesus Macaques (Macaca mulatta)

HIV-infected people develop reproducible disruptions in their gastrointestinal microbiota. Despite the suppression of HIV viremia via long-term antiretroviral therapy (ART), alterations still occur in gut microbial diversity and the commensal microbiota. Mounting evidence suggests these microbial changes lead to the development of gut dysbiosis-persistent inflammation that damages the gut mucosa-and correlate with various immune defects. In this study, we examined how early ART intervention influences microbial diversity in SIV-infected rhesus macaques. Using 16S rRNA sequencing, we defined the fecal microbiome in macaques given daily ART beginning on either 3 or 7 d after SIV infection (dpi) and characterized changes in composition, α diversity, and β diversity from before infection through 112 dpi. The dominant phyla in the fecal samples before infection were Bacteroidetes, Firmicutes, Spirochaetes, and Proteobacteria. After SIV infection and ART, the relative abundance of Firmicutes and Bacteroidetes did not change significantly. Significant reductions in α diversity occurred across time when ART was initiated at 3 dpi but not at 7 dpi. Principal coordinate analysis of samples revealed a divergence in β diversity in both treatment groups after SIV infection, with significant differences depending on the timing of ART administration. These results indicate that although administration of ART at 3 or 7 dpi did not substantially alter fecal microbial composition, the timing of early ART measurably altered phylogenetic diversity.

Shifts in water column microbial composition associated to lakes with different trophic conditions: "Lagunas de Montebello" National Park, Chiapas, México

Eutrophication is a global problem causing the reduction of water quality and the loss of ecosystem goods and services. The lakes of the "Lagunas de Montebello" National Park (LMNP), Chiapas, Mexico, not only represent unique and beautiful natural scenic sites in southern Mexico but are also a national protected area and RAMSAR site. Unfortunately, some of these lakes started showing eutrophication signs since 2003. Anthropogenic activities (e.g., land-use change from forested to agricultural and urban development) are leading to water quality and trophic state alterations of the lakes of the LMNP. This study shows the results of a coupled limnological characterization and high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene to analyze the microbial composition of the water column in a set of oligotrophic and eutrophic lakes. Chlorophyll a (Chl-a) was the main environmental parameter correlated with the trophic conditions of the lakes. Although the microbial diversity was similar, the microbial composition changed significantly from oligo to eutrophic lakes. Proteobacteria, Firmicutes, and Cyanobacteria were the main components of oligotrophic lakes, and Cyanobacteria, Proteobacteria, and Bacteroidetes of eutrophic lakes. While Acinetobacter (Proteobacteria) and Cyanobium (a unicellular cyanobacterium) dominated in oligotrophic lakes, the filamentous, bloom-forming, and toxin-producing cyanobacteria Planktothrix was the dominant genus in eutrophic lakes. High-throughput sequencing allowed the detection of changes in the composition of the microbial component in oligotrophic lakes, suggesting a shift towards eutrophication, highlighting the relevance of sensitive monitoring protocols of these ecosystems to implement remediation programs for eutrophicated lakes and conservation strategies for those yet pristine.

Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing

Black soldier fly larvae (BSFL) belong to the most widely reared insects as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members of Enterococcus, Klebsiella, Morganella, Providencia, and Scrofimicrobium. Further, the factors 'Study', 'Age' and 'Feed' (i.e. rearing substrate of the larvae) significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics analysis pipeline can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect rearing conditions and substrates.

Soil bacteria around a derelict tailings pile with different metal pollution gradients: community composition, metal tolerance and influencing factors

Bacteria play a vital role in ecological processes of soil contaminated by heavy metals. Here, soil sampling was carried out around a tailings pile contaminated to different degrees by cadmium (Cd), lead (Pb) and arsenic (As). The bacteria in the soil were cultured, separated and purified on Luria-Bertani medium, and the changes in bacterial communities in soils with different pollution levels were analysed with 16S rRNA sequencing. Bacillus pacificus strain MZ520364 was found to be highly tolerant to Cd, Pb and As, and single-metal and multimetal tolerance experiments were further conducted with this strain. The results obtained from alpha diversity and operational taxonomic unit (OTU) statistical analyses showed a significant difference in bacterial composition among soils with different metal pollution levels, and the highest bacterial diversity was found at the most severely polluted site. Evidence from variance partitioning analysis (VPA) and the Spearman correlation heatmap analysis showed that the leading factors affecting bacterial community composition were cation exchange content (CEC), pH, total Zn, total As, and available As concentrations in soil. Additionally, in the single-metal treatments, B. pacificus MZ520364 could tolerate 600 mg/L Cd²⁺, 1000 mg/L Pb²⁺ or 700 mg/L As³⁺. When Cd, Pb and As coexisted, the best growth of B. pacificus MZ520364 was present at 120 mg/L Cd²⁺, 200 mg/L Pb²⁺ and 150 mg/L As³⁺. The effect of Cd, Pb and As on the growth of the strain followed the order of Cd > As > Pb, and the heavy metal combination showed more toxicity than single metals. In summary, our results revealed the ecological impact of soil physicochemical properties on the diversity and richness of soil bacterial communities and suggested that B. pacificus MZ520364 may be used for the remediation of Cd-Pb-As co-contaminated soil.

Effects of emerging contaminants and heavy metals on variation in bacterial communities in estuarine sediments

Emerging contaminants (ECs) and heavy metals (HMs) are universally present together in estuarine sediments; despite this, their effects on microbial communities have been widely studied separately, rather than in consort. In this study, the combined effects of ECs and HMs on microbial communities were investigated in sediments from 11 major river estuaries around the Bohai Sea, China. Proteobacteria, Bacteroidetes, and Firmicutes were the dominant phyla in the sediments. Using Shannon indices, total phosphorus and total organic carbon were shown to affect microbial community structure. Redundancy analysis of microbial variation implicated Cd and As as the greatest pollutants, followed by Mn, Fe, Zn and Cu; no impacts from galaxolide (HHCB) and tonalide (AHTN) were found. Correlation analysis demonstrated that the concentration of ECs increased the abundance of certain bacteria (e.g., Haliangium, Altererythrobacter, Gaiella and Erythrobacter), and therefore these can be used as potential contamination indicators. Shannon indices and Chao1 indices showed that there were differences in the richness and diversity of bacterial communities in the sediments of 11 rivers. The principal coordinate analysis displayed higher similarity of bacterial community composition in estuarine sediments in Liaoning province than other regions. The results can be used to predict changes in estuary ecosystems to maintain their ecological balance and health.

Metagenomic analysis of bacterial communities of Wadi Namar Lake, Riyadh, Saudi Arabia

Wadi Namar lake is a new touristic attraction area in the south of Riyadh. Human activities around the lake may lead to changes in water quality with subsequent changes in microenvironment components including microbial diversity. The current study was designed to assess possible changes in bacterial communities of the water at Wadi Namar Lake. Therefore, water samples were collected from three different locations along the lake: L1 (no human activities, no plants), L2 (no human activity, some plants) and L3 (human activities, municipal wastes and some plants). The total DNA of the samples was extracted and subjected to 16S rDNA sequencing and metagenomic analysis; water pH, electrical conductivity (EC), total dissolved solids (TDS) as well as the concentration of Na+1, K+1, Cl-1 and total N were analysed. Metagenomic analysis showed variations in relative abundance of 17 phyla, 31 families, 43 genera and 19 species of bacteria between the locations. Proteobacteria was the most abundant phylum in all locations; however, its highest abundance was in L1. Planctomycete phylum was highly abundant in L1 and L3, while its abundance in L2 was low. The phyla Acidobacteria, Candidatus Saccharibacteria, Nitrospirae and Chloroflexi were associated with high TDS, EC, K+1 and Cl-1 concentrations in L3; various human activities around this location had possibly affected microbial diversity. Current study results help in recognising the structure of bacterial communities at Wadi Namar Lake in relation to their surroundings for planning to environment protection and future restoration of affected ecosystems.

Microbial Identification Using rRNA Operon Region: Database and Tool for Metataxonomics with Long-Read Sequence

Recent development of long-read sequencing platforms has enabled researchers to explore bacterial community structure through analysis of full-length 16S rRNA gene (∼1,500 bp) or 16S-ITS-23S rRNA operon region (∼4,300 bp), resulting in higher taxonomic resolution than short-read sequencing platforms. Despite the potential of long-read sequencing in metagenomics, resources and protocols for this technology are scarce. Here, we describe MIrROR, the database and analysis tool for metataxonomics using the bacterial 16S-ITS-23S rRNA operon region. We collected 16S-ITS-23S rRNA operon sequences extracted from bacterial genomes from NCBI GenBank and performed curation. A total of 97,781 16S-ITS-23S rRNA operon sequences covering 9,485 species from 43,653 genomes were obtained. For user convenience, we provide an analysis tool based on a mapping strategy that can be used for taxonomic profiling with MIrROR database. To benchmark MIrROR, we compared performance against publicly available databases and tool with mock communities and simulated data sets. Our platform showed promising results in terms of the number of species covered and the accuracy of classification. To encourage active 16S-ITS-23S rRNA operon analysis in the field, BLAST function and taxonomic profiling results with 16S-ITS-23S rRNA operon studies, which have been reported as BioProject on NCBI are provided. MIrROR (http://mirror.egnome.co.kr/) will be a useful platform for researchers who want to perform high-resolution metagenome analysis with a cost-effective sequencer such as MinION from Oxford Nanopore Technologies. IMPORTANCE Metabarcoding is a powerful tool to investigate community diversity in an economic and efficient way by amplifying a specific gene marker region. With the advancement of long-read sequencing technologies, the field of metabarcoding has entered a new phase. The technologies have brought a need for development in several areas, including new markers that long-read can cover, database for the markers, tools that reflect long-read characteristics, and compatibility with downstream analysis tools. By constructing MIrROR, we met the need for a database and tools for the 16S-ITS-23S rRNA operon region, which has recently been shown to have sufficient resolution at the species level. Bacterial community analysis using the 16S-ITS-23S rRNA operon region with MIrROR will provide new insights from various research fields.

Mechanisms of immune activation and regulation: lessons from melanoma

Melanoma, a skin cancer that develops from pigment cells, has been studied intensively, particularly in terms of the immune response to tumours, and has been used as a model for the development of immunotherapy. This is due, in part, to the high mutational burden observed in melanomas, which increases both their immunogenicity and the infiltration of immune cells into the tumours, compared with other types of cancers. The immune response to melanomas involves a complex set of components and interactions. As the tumour evolves, it accumulates an increasing number of genetic and epigenetic alterations, some of which contribute to the immunogenicity of the tumour cells and the infiltration of immune cells. However, tumour evolution also enables the development of resistance mechanisms, which, in turn, lead to tumour immune escape. Understanding the interactions between melanoma tumour cells and the immune system, and the evolving changes within the melanoma tumour cells, the immune system and the microenvironment, is essential for the development of new cancer therapies. However, current research suggests that other extrinsic factors, such as the microbiome, may play a role in the immune response to melanomas. Here, we review the mechanisms underlying the immune response in the tumour and discuss recent advances as well as strategies for treatment development.

Novel primers for 16S rRNA gene-based archaeal and bacterial community analysis in oceanic trench sediments

High-throughput sequencing of the 16S ribosomal RNA (16S rRNA) gene has been successfully applied to explore the microbial structure and dynamics in various environments. The distinctive microbial communities in oceanic trench sediments are expected because of the extremely high pressure and V-shape topology that caused the isolation from the other marine sediments. However, they have only been primarily targeted using 'universal' primers that provide variable performances for different environments. It is necessary to design specific primers to improve the detection resolution of unique microbial groups in oceanic trenches. Here, we designed one pair of bacterial and two pairs of archaeal specific primers based on 16S rRNA gene full-length sequences that truly come from trench sediment and tested their performances in 30 oceanic trench sediment samples. An in silico analysis showed that the V3-V4 hypervariable region was the most informative and representative for oceanic trench microbial groups. Compared with the 'universal' primers, 46 bacterial families were only detected by newly designed primer B344F/B749R, and eight archaeal families were only detected by the newly designed primer A306F/A713R which covered the one or two orders of magnitude more ASVs (amplicon sequence variants) (1,470,216) in the tested total 30 samples. Moreover, A306F/A713R had the largest number of observed ASVs suggesting its better performance in discovering more archaeal species which were easily ignored in universal primer-based experiments for oceanic trench sediments. The novel primers designed in this research could be a better option to access the unique microbial communities in extreme oceanic trench sediments.Key points• Defining V3-V4 as the most adequate hypervariable region for archaea and bacteria from oceanic trench sediments.• Three sets of bacterial and archaeal primers appear validity and advantage in revealing the real trench microbial communities.• The novel primers provide a better option to specifically detect the unique microbial communities in extreme oceanic trench sediments.

Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis

Southern River Terrapin, Batagur affinis, is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this study aimed to characterise and compare the faecal bacterial community between captive and wild B. affinis using metabarcoding approaches. A total of seven faeces samples were collected from captive (N = 5) and wild (N = 2) adult B. affinis aseptically, crossing the East and West coast of peninsular Malaysia. The DNA was extracted from the faeces samples, and the 16S rRNA gene (V3-V4 region) was amplified using polymerase chain reaction (PCR). The amplicon was further analysed using SILVA and DADA2 pipelines. In total, 297 bacterial communities taxonomic profile (phylum to genus) were determined. Three phyla were found in high abundance in all faeces samples, namely Firmicutes (38.69%), Bacteroidetes (24.52%), and Fusobacteria (6.95%). Proteobacteria were detected in all faeces samples (39.63%), except the wild sample, KBW3. Under genus level, Cetobacteriumwas found as the most abundant genus (67.79%), followed by Bacteroides (24.56%) and Parabacteroides (21.78%). The uncultured genus had the highest abundance (88.51%) even though not detected in the BK31 and KBW2 samples. The potential probiotic genera (75.00%) were discovered to be more dominant in B. affinis faeces samples. Results demonstrated that the captive B. affinis faeces samples have a greater bacterial variety and richness than wild B. affinis faeces samples. This study has established a starting point for future investigation of the gut microbiota of B. affinis.

Inactivation of Antibiotic-Resistant Bacteria in Wastewater by Ozone-Based Advanced Water Treatment Processes

The inactivating effect of ozone (O₃)-based advanced oxidation processes (AOPs) (O₃/H₂O₂, O₃/UV, and O₃/UV/H₂O₂ systems) on antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB) in sewage treatment plant (STP) wastewater was investigated. The AMRB were grouped into six classes: carbapenem-resistant Enterobacteriaceae (CRE), extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E), multidrug-resistant Acinetobacter (MDRA), multidrug-resistant Pseudomonas aeruginosa (MDRP), methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococcus (VRE); these classes constituted the World Health Organization (WHO) global priority list of AMRB. The results indicate that O₃-based advanced wastewater treatment inactivated all AMRB and AMSB (>99.9%) after 10 min of treatment, and significant differences (p < 0.5) were not observed in the disinfection of AMRB and AMSB by each treatment. Altered taxonomic diversity of micro-organisms based on 16S rRNA gene sequencing via O₃/UV and O₃/UV/H₂O₂ treatment showed that advanced wastewater treatments not only inactivated AMRB but also removed antimicrobial resistance genes (AMRGs) in the wastewater. Consequently, this study recommends the use of advanced wastewater treatments for treating the STP effluent, reducing environmental pollution, and alleviating the potential hazard to human health caused by AMRB, AMSB, and infectious diseases. Overall, this study provides a new method for assessing environmental risks associated with the spread of AMRB and AMSB in aquatic environments, while keeping the water environment safe and maintaining human health.

Factors affecting seasonal variation of microbial community structure in Hulun Lake, China

Microbial communities play an important role in water quality regulation and biogeochemical cycling in freshwater ecosystems. However, there is a lack of research on the seasonal variation in lake water microorganisms in cold environments. In this study, 16S rRNA gene high-throughput sequencing was used to explore the microbial community and its influencing factors in Hulun Lake water during different seasons. The results showed that Proteobacteria, Actinobacteria, and Bacteroidetes were the most important phyla in the microbial community of Hulun Lake, but they had significant seasonal differences in their distribution. In addition, significant seasonal differences were observed in the α diversity of microorganisms, with bacterial diversity being higher in winter than in summer. Changes in environmental variables were significantly correlated with changes in the microbial community, and the rapid changes in temperature, pH, and dissolved oxygen are potentially the major factors influencing seasonal bacterial diversity trends. The findings of the present study enhance our understanding of the microbial communities in alpine lake ecosystems and are of great significance for the management and protection of lake ecosystems.

Does diet breadth affect the complexity of the phytophagous insect microbiota? The case study of Chrysomelidae

Chrysomelidae is a family of phytophagous insects with a highly variable degree of trophic specialization. The aim of this study is to test whether species feeding on different plants (generalists) harbour more complex microbiotas than those feeding on a few or a single plant species (specialists). The microbiota of representative leaf beetle species was characterized with a metabarcoding approach targeting V1–V2 and V4 regions of the bacterial 16S rRNA. Almost all the analysed species harbour at least one reproductive manipulator bacteria (e.g., Wolbachia, Rickettsia). Two putative primary symbionts, previously isolated only from a single species (Bromius obscurus), have been detected in two species of the same subfamily, suggesting a widespread symbiosis in Eumolpinae. Surprisingly, the well‐known aphid symbiont Buchnera is well represented in the microbiota of Orsodacne humeralis. Moreover, in this study, using Hill numbers to dissect the components of the microbiota diversity (abundant and rare bacteria), it has been demonstrated that generalist insect species harbour a more diversified microbiota than specialists. The higher microbiota diversity associated with a wider host‐plant spectrum could be seen as an adaptive trait, conferring new metabolic potential useful to expand the diet breath, or as a result of environmental stochastic acquisition conveyed by diet.

Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1-V2 and V3-V4 primer sets

BACKGROUND

16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using the modified V1-V2 (V12) and the standard V3-V4 primer (V34) sets to optimize the gut microbiota analysis protocol.

RESULTS

QIIME1 and QIIME2 analysis revealed a higher number of unclassified representative sequences in the V34 data than in the V12 data. The comparison of bacterial composition demonstrated that at the phylum level, Actinobacteria and Verrucomicrobia were detected at higher levels with V34 than with V12. Among these phyla, we observed higher relative compositions of Bifidobacterium and Akkermansia with V34. To estimate the actual abundance, we performed quantitative real-time polymerase chain reaction (qPCR) assays for Akkermansia and Bifidobacterium. We found that the abundance of Akkermansia as detected by qPCR was close to that in V12 data, but was markedly lower than that in V34 data. The abundance of Bifidobacterium detected by qPCR was higher than that in V12 and V34 data.

CONCLUSIONS

These results indicate that the bacterial composition derived from the V34 region might differ from the actual abundance for specific gut bacteria. We conclude that the use of the modified V12 primer set is more desirable in the 16S analysis of the Japanese gut microbiota.

On-site chlorination responsible for effective disinfection of wastewater from hospital

Both hospital effluent and a model sewage treatment plant (STP) wastewater prepared by mixing STP influent and STP secondary effluent at a volume ratio of 1:9 were directly treated with chlorine for investigation of their effects on disinfection of antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB). The overall results indicate that the chlorine disinfection effectively inactivated the majority of AMRB and AMSB, expect for MRSA and Staphylococcus aureus in both wastewaters. No significant differences could further be observed in the taxonomic diversity of micro-organisms after the treatment. The degrees of disinfection given by the direct chlorination were comparable to those attained by combination of conventional activated sludge process and additional chlorine treatment at the STP. The results of this study evoked a recommendation to operate local chlorination treatment directly for the wastewater from medicinal facilities prior to its flow into the STP as sewage. Although additional disinfection treatment at the STP seems necessary to remove the recalcitrant MRSA and Staphylococcus aureus, the present study desirably contributes to a great reduction of the loads of STP and urgent prevention of spreading of infectious diseases in the present state.

Evaluation of microbial diversity of three recreational water bodies using 16S rRNA metagenomic approach

Surface water plays a significant role in world development by promoting economic growth and health benefits to humans and animals whose lives depend on good water quality in the ecosystem. Thus, this study investigated the differences in physical and chemical properties of surface water from two lakes (Lakes Jackson and Talquin) and a pond (Pedrick Pond). Also, the influence of environmental factors on the microbial communities that live within the water environment was examined. Genomic DNA was extracted from the water samples collected and 16S rRNA sequencing method was employed to characterize the microbial community compositions across the three locations. The results obtained suggest that the water sources met the recommended recreational water quality criteria standard for clean water. Overall, Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes were the main bacterial phyla present in the communities, while Archaea was mainly dominated by Euryachaeota. Pressure, conductivity, temperature, dissolved oxygen (DO), and pH accounted for 74.2% of the variation in the distribution of the microbial community in the three locations (P < 0.05), while 58.2% of the variation in the microbial community distribution was accounted for by pressure and conductivity. The high temperature observed in the Pedrick Pond correlated with the distribution of genera hgcl_clades and Legionella. While in Lake Talquin, water conductivity was significantly associated with the abundance of Cyanobium_PCC_6307, Sediminibacterium, and Conexibacter. The results from this study indicate that the microbial communities in the two lakes are different from the pond and all the environmental variables accounted for a significant portion of the total variation, but pressure, conductivity, and temperature are more important factors due to significant correlation with the distribution of the microbial communities.

Identifying biases and their potential solutions in human microbiome studies

Advances in DNA sequencing technology have vastly improved the ability of researchers to explore the microbial inhabitants of the human body. Unfortunately, while these studies have uncovered the importance of these microbial communities to our health, they often do not result in similar findings. One possible reason for the disagreement in these results is due to the multitude of systemic biases that are introduced during sequence-based microbiome studies. These biases begin with sample collection and continue to be introduced throughout the entire experiment leading to an observed community that is significantly altered from the true underlying microbial composition. In this review, we will highlight the various steps in typical sequence-based human microbiome studies where significant bias can be introduced, and we will review the current efforts within the field that aim to reduce the impact of these biases. Video abstract.

Effects of natural sunlight on antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB) in wastewater and river water

The effects of natural sunlight on antimicrobial-resistant bacteria (AMRB) and antimicrobial-susceptible bacteria (AMSB) were investigated in three types of water: sewage treatment plant (STP) influent, STP secondary effluent, and river water in an urban area of Japan. The AMRB were grouped into six classes: carbapenem-resistant Enterobacteriaceae (CRE), extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E), multi-drug-resistant Acinetobacter (MDRA), multi-drug-resistant Pseudomonas aeruginosa (MDRP), methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococcus (VRE). The amount of each group of bacteria present was estimated using specific chromogenic agar formulations. AMRB were detected in all water samples, with 13-2,407 colony-forming units (CFU)/mL in the STP influent, N.D. to 202 CFU/mL in the secondary STP effluent, and N.D. to 207 CFU/mL in the river water. The distribution profiles of the AMSB in water samples were similar to those of AMRB. The degree to which AMRB and AMSB present in the river water were inactivated by natural sunlight was tested as the main aim of this study. Irradiation by natural sunlight was found to inactivate almost 100% of all the target AMRB after 5 h of exposure, with no significant differences (P < 0.05) observed in the effects that sunlight had on AMSB and AMRB. Analysis of the bacterial community structure based on 16S rRNA gene sequencing showed that the structure of the bacterial community was apparently not affected by the exposure to sunlight. In addition, the taxonomic diversity in the STP secondary effluent did not change as a result of additional disinfection with chlorine. The results of this study suggest that it is possible that exposure to sunlight could be used as an alternative to disinfection via chlorine. To our knowledge, this is the first report to demonstrate the mitigation of AMSB and AMRB pollution in a river environment via the exposure to natural sunlight.

Identification the source of fecal contamination for geographically unassociated samples with a statistical classification model based on support vector machine

The bacterial diversity and corresponding biological significance revealed by high-throughput sequencing contribute massive information to source tracking of fecal contamination. The performances of classification models on predicting the fecal source of geographical local and foreign samples were examined herein, by applying support vector machine (SVM) algorithm. Random forest (RF) and Adaboost were applied for comparison as well. Discriminatory sequences were selected from Clostridiale, Bacteroidales, or Lactobacillales bacterial groups using extremely randomized trees (ExtraTrees). 1.51-12.64% of the unique sequences in the original library composed the representative markers, and they contributed 70% of the discrepancies between source microbiomes. The overall accuracy of the SVM model and the RF model on local samples was 96.08% and 98.04%, respectively, higher than that of the Adaboost (90.20%). As for the non-local samples, the SVM assigned most of the fecal samples into the correct category while several false-positive judgments occurred in closely related groups. The results in this paper suggested that the SVM was a time-saving and accurate method for fecal source tracking in contaminated water body with the potential capability of executing tasks based on geographically unassociated samples, and underlined the necessity of qPCR analysis for accurate detection of human source pollution.

The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology

Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.

Bacterial community composition and diversity in the ballast water of container ships arriving at Yangshan Port, Shanghai, China

Ballast water is a major vector of invasion by protozoans and metazoans. Bacterial invasion is less-well understood. We surveyed the bacterial diversity of ballast water from 26 container ships arriving at the Yangshan Deepwater Port, Shanghai, China during 2015-2016. We characterized the ballast microbiome using high-throughput sequencing (HTS) based on V4-V5 region of 16S rRNA genes. We simultaneously monitored physicochemical parameters of the ballast water, including temperature, pH, dissolved oxygen (DO), salinity, turbidity, total suspended solid (TSS), particulate organic carbon (POC), NO₂, NH₄, PO₄. Proteobacteria was the dominant phylum, comprising more than 50% of the OTUs of almost all vessels, followed by Bacteroidetes (12.08%), Actinobacteria (4.86%) Planctomycetes (3.24%) and Cyanobacteria (1.95%). The relative abundance of Cyanobacteria differed among vessels. It was negatively correlated with temperature, NO₃, pH, TSS, PO₄, and turbidity and positively correlated with NH₄, POC. The genus Synechococcus was the most common Cyanobacteria in our results. Escherichia coli were relatively rare; they are indicator-species of D-2 standards published by the IMO. The relative abundance of the genus Vibrio ranged from 0.003% to 24.88% among different vessels. Our results showed that HTS was able to profile the bacterial communities in ballast-waters, even when the approach was restricted by technical and other obstacles.

Sediment-associated bacterial community and predictive functionalities are influenced by choice of 16S ribosomal RNA hypervariable region(s): An amplicon-based diversity study

Meta-omics approaches such as high-throughput sequencing of 16S hypervariable region(s) [HVR(s)] is extensively applied for profiling microbial community. Several studies have deciphered the influence of HVR(s) on bacterial diversity; most of these were devoted to human body habitats. Extent to which targeted HVR(s) influences the diversity estimates of environmental samples is rather unclear. Here, we evaluated the performance of five widely used universal primer pairs spanning V1-V3, V3-V4, V4, V5-V6 and V7-V9 HVRs to characterize bacterial diversity and predictive functionality of complex marine sediments. Obtained results revealed that the HVR(s) V4 and V5-V6 represented the higher species richness than others while, V1-V3 and V7-V9 were unsuccessful to detect Bacteroidetes and Planctomycetes. Further, PICRUSt analysis showed that the selected HVR(s) also had significant impact on the predictive functional profile. Conclusively, this study proved that HVR selection has a profound effect on overall results and thus should be selected with utmost caution.

Host Genetic Background and Gut Microbiota Contribute to Differential Metabolic Responses to Fructose Consumption in Mice

BACKGROUND

It is unclear how high fructose consumption induces disparate metabolic responses in genetically diverse mouse strains.

OBJECTIVE

We aimed to investigate whether the gut microbiota contributes to differential metabolic responses to fructose.

METHODS

Eight-week-old male C57BL/6J (B6), DBA/2J (DBA), and FVB/NJ (FVB) mice were given 8% fructose solution or regular water (control) for 12 wk. The gut microbiota composition in cecum and feces was analyzed using 16S ribosomal DNA sequencing, and permutational multivariate ANOVA (PERMANOVA) was used to compare community across mouse strains, treatments, and time points. Microbiota abundance was correlated with metabolic phenotypes and host gene expression in hypothalamus, liver, and adipose tissues using Biweight midcorrelation. To test the causal role of the gut microbiota in determining fructose response, we conducted fecal transplants from B6 to DBA mice and vice versa for 4 wk, as well as gavaged antibiotic-treated DBA mice with Akkermansia for 9 wk, accompanied with or without fructose treatment.

RESULTS

Compared with B6 and FVB, DBA mice had significantly higher Firmicutes to Bacteroidetes ratio and lower baseline abundance of Akkermansia and S24-7 (P < 0.05), accompanied by metabolic dysregulation after fructose consumption. Fructose altered specific microbial taxa in individual mouse strains, such as a 7.27-fold increase in Akkermansia in B6 and 0.374-fold change in Rikenellaceae in DBA (false discovery rate <5%), which demonstrated strain-specific correlations with host metabolic and transcriptomic phenotypes. Fecal transplant experiments indicated that B6 microbes conferred resistance to fructose-induced weight gain in DBA mice (F = 43.1, P < 0.001), and Akkermansia colonization abrogated the fructose-induced weight gain (F = 17.8, P < 0.001) and glycemic dysfunctions (F = 11.8, P = 0.004) in DBA mice.

CONCLUSIONS

Our findings support that differential microbiota composition between mouse strains is partially responsible for host metabolic sensitivity to fructose, and that Akkermansia is a key bacterium that confers resistance to fructose-induced metabolic dysregulation.