Ultrafast clustering algorithms for metagenomic sequence analysis

Potential and challenge in accelerating high-value conversion of CO2 in microbial electrosynthesis system via data-driven approach

Microbial electrosynthesis for CO2 utilization (MESCU) producing valuable chemicals with high energy density has garnered attention due to its long-term stability and high coulombic efficiency. The data-driven approaches offer a promising avenue by leveraging existing data to uncover the underlying patterns. This comprehensive review firstly uncovered the potentials of utilizing data-driven approaches to enhance high-value conversion of CO2 via MESCU. Firstly, critical challenges of MESCU advancing have been identified, including reactor configuration, cathode design, and microbial analysis. Subsequently, the potential of data-driven approaches to tackle the corresponding challenges, encompassing the identification of pivotal parameters governing reactor setup and cathode design, alongside the decipheration of omics data derived from microbial communities, have been discussed. Correspondingly, the future direction of data-driven approaches in assisting the application of MESCU has been addressed. This review offers guidance and theoretical support for future data-driven applications to accelerate MESCU research and potential industrialization.

Low electric current in a bioelectrochemical system facilitates ethanol production from CO using CO-enriched mixed culture

Fossil resources must be replaced by renewable resources in production systems to mitigate green-house gas emissions and combat climate change. Electro-fermentation utilizes a bioelectrochemical system (BES) to valorize industrial and municipal waste. Current electro-fermentation research is mainly focused on microbial electrosynthesis using CO2 for producing commodity chemicals and replacing petroleum-based infrastructures. However, slow production rates and low titers of metabolites during CO2-based microbial electrosynthesis impede its implementation to the real application in the near future. On the other hand, CO is a highly reactive gas and an abundant feedstock discharged from fossil fuel-based industry. Here, we investigated CO and CO2 electro-fermentation, using a CO-enriched culture. Fresh cow fecal waste was enriched under an atmosphere of 50% CO and 20% CO2 in N2 using serial cultivation. The CO-enriched culture was dominated by Clostridium autoethanogenum (≥89%) and showed electro-activity in a BES reactor with CO2 sparging. When 50% CO was included in the 20% CO2 gas with 10 mA applied current, acetate and ethanol were produced up to 12.9 ± 2.7 mM and 2.7 ± 1.1 mM, respectively. The coulombic efficiency was estimated to 148% ± 8% without an electron mediator. At 25 mA, the culture showed faster initial growth and acetate production but no ethanol production, and only at 86% ± 4% coulombic efficiency. The maximum optical density (OD) of 10 mA and 25 mA reactors were 0.29 ± 0.07 and 0.41 ± 0.03, respectively, whereas it was 0.77 ± 0.19 without electric current. These results show that CO electro-fermentation at low current can be an alternative way of valorizing industrial waste gas using a bioelectrochemical system.

Comparison of Metabarcoding and Microscopy Methodologies to Analyze Diatom Communities in Five Estuaries Along the Southern Coast of the Korean Peninsula

The study of microalgal communities is critical for understanding aquatic ecosystems. These communities primarily comprise diatoms (Heterokontophyta), with two methods commonly used to study them: Microscopy and metabarcoding. However, these two methods often deliver different results; thus, their suitability for analyzing diatom communities is frequently debated and evaluated. This study used these two methods to analyze the diatom communities in identical water samples and compare the results. The taxonomy of the species constituting the diatom communities was confirmed, and both methods showed that species belonging to the orders Bacillariales and Naviculales (class Bacillariophyceae) are the most diverse. In the lower taxonomic levels (family, genus, and species), microscopy tended to show a bias toward detecting diatom species (Nitzschia frustulum, Nitzschia inconspicua, Nitzschia intermedia, Navicula gregaria, Navicula perminuta, Navicula recens, Navicula sp.) belonging to the Bacillariaceae and Naviculaceae families. The results of the two methods differed in identifying diatom species in the communities and analyzing their structural characteristics. These results are consistent with the fact that diatoms belonging to the genera Nitzschia and Navicula are abundant in the communities; furthermore, only the Illumina MiSeq data showed the abundance of the Melosira and Entomoneis genera. The results obtained from microscopy were superior to those of Illumina MiSeq regarding species-level identification. Based on the results obtained via microscopy and Illumina MiSeq, it was revealed that neither method is perfect and that each has clear strengths and weaknesses. Therefore, to analyze diatom communities effectively and accurately, these two methods should be combined.

Resistant starch-enriched brown rice exhibits prebiotic properties and enhances gut health in obese mice

Resistant starch serves as a prebiotic in the large intestine, aiding in the maintenance of a healthy intestinal environment and mitigating associated chronic illnesses. This study aimed to investigate the impact of resistant starch-enriched brown rice (RBR) on intestinal health and functionality. We assessed changes in resistant starch concentration, structural alterations, and branch chain length distribution throughout the digestion process using an in vitro model. The efficacy of RBR in the intestinal environment was evaluated through analyses of its prebiotic potential, effects on intestinal microbiota, and intestinal function-related proteins in obese animals fed a high-fat diet. RBR exhibited a higher yield of insoluble fraction in both the small and large intestines compared to white and brown rice. The total digestible starch content decreased, while the resistant starch content significantly increased during in vitro digestion. Furthermore, RBR notably enhanced the growth of four probiotic strains compared to white and brown rice, displaying higher proliferation activity than the positive control, FOS. Notably, consumption of RBR by high-fat diet-induced obese mice suppressed colon shortening, increased Bifidobacteria growth, and improved intestinal permeability. These findings underscore the potential prebiotic and gut health-promoting attributes of RBR, offering insights for the development of functional foods aimed at preventing gastrointestinal diseases.

The hidden RNA viruses in Blattodea (cockroaches and termites)

The insect order Blattodea (cockroaches and termites) has drawn substantial research attention for their dietary habits and lifestyle of living with or around humans. In the present study, we focused on the discovery of RNA viruses hidden in Blattodea insects using the publicly available RNA sequencing datasets. Overall, 136 distinctive RNA viruses were identified from 36 Blattodea species, of which more than 70 % were most closely related to the invertebrate-associated viral groups within Picornavirales, Sobelivirales, Bunyaviricetes, Jingchuvirales, Durnavirales, Lispiviridae, Orthomyxoviridae, Permutotetraviridae, Flaviviridae and Muvirales. Several viruses were associated with pathogens of vertebrates (Paramyxoviridae), plants (Tymovirales), protozoa (Totiviridae), fungi (Narnaviridae) and bacteria (Norzivirales). Collectively, 93 complete or near-complete viral genomes were retrieved from the datasets, and several viruses appeared to have remarkable temporal and spatial distributions. Interestingly, the newly identified Periplaneta americana dicistrovirus displayed a remarkable distinct bicistronic genome arrangement from the well-recognized dicistroviruses with the translocated structural and non-structural polyprotein encoding open reading frames over the genome. These results significantly enhance our knowledge of RNA virosphere in Blattodea insects, and the novel genome architectures in dicistroviruses and other RNA viruses may break our stereotypes in the understanding of the genomic evolution and the emergence of potential novel viral species.

Insights into the seasonal changes in the taxonomic and functional diversity of bacteria in the eastern Arabian Sea: Shotgun metagenomics approach

The eastern Arabian Sea (EAS) is known for its unique oceanographic features such as the seasonal monsoonal winds, upwelling of nutrient-rich waters and a significant increase in primary productivity during the monsoon season. In this study, we utilised the shotgun metagenomics approach to determine the seasonal variations in bacterial taxonomic and functional profiles during the non-monsoon and monsoon seasons in the EAS. Significant seasonal variations in the bacterial community structure were observed at the phylum and genera levels. These findings also correspond with seasonal shifts in the functional profiles of the bacterial communities based on the variations of genes encoding enzymes associated with different metabolic pathways. Pronounced seasonal variation of bacterial taxa was evident with an increased abundance of Idiomarina, Marinobacter, Psychrobacter and Alteromonas of Proteobacteria, Bacillus and Staphylococcus of Firmicutes during the non-monsoon season. These taxa were linked to elevated nucleotide and amino acid biosynthesis, amino acid and lipid degradation. Conversely, during the monsoon, the taxa composition changed with Alteromonas, Candidatus Pelagibacter of Proteobacteria and Cyanobacteria Synechococcus; contributing largely to the amino acid and lipid biosynthesis, fermentation and inorganic nutrient metabolism which was evident from functional analysis. Regression analysis confirmed that increased seasonal primary productivity significantly influenced the abundance of genes associated with carbohydrate, protein and lipid metabolism. These highlight the pivotal role of seasonal changes in primary productivity in shaping the bacterial communities, their functional profiles and driving the biogeochemical cycling in the EAS.

Circulating TMAO, the gut microbiome and cardiometabolic disease risk: an exploration in key precursor disorders

BACKGROUND

Elevations in the gut metabolite trimethylamine-N-oxide (TMAO) have been linked to cardiovascular and metabolic diseases. Whether elevated TMAO levels reflect early mechanistic involvement or a sequela of evolving disease awaits elucidation. The purpose of this study was to further explore these potential associations.

METHODS

We investigated relationships between circulating levels of TMAO and its pre-cursor substrates, dietary factors, gut microbiome profiles and disease risk in individuals with a Healthy BMI (18.5 < BMI < 25, n = 41) or key precursor states for cardiometabolic disease: Overweight (25 < BMI < 30 kg/m2, n = 33), Obese (BMI > 30, n = 27) and Metabolic Syndrome (MetS; ≥ 3 ATPIII report criteria, n = 39).

RESULTS

Unexpectedly, plasma [TMAO] did not vary substantially between groups (means of 3-4 µM; p > 0.05), although carnitine was elevated in participants with MetS. Gut microbial diversity and Firmicutes were also significantly reduced in the MetS group (p < 0.05). Exploratory analysis across diverse parameters reveals significant correlations between circulating [TMAO] and seafood intake (p = 0.007), gut microbial diversity (p = 0.017-0.048), and plasma [trimethylamine] (TMA; p = 0.001). No associations were evident with anthropometric parameters or cardiometabolic disease risk. Most variance in [TMAO] within and between groups remained unexplained.

CONCLUSIONS

Data indicate that circulating [TMAO] may be significantly linked to seafood intake, levels of TMA substrate and gut microbial diversity across healthy and early disease phenotypes. However, mean concentrations remain < 5 µM, with little evidence of links between TMAO and cardiometabolic disease risk. These observations suggest circulating TMAO may not participate mechanistically in cardiometabolic disease development, with later elevations likely a detrimental sequela of extant disease.

A novel multi-task learning network for skin lesion classification based on multi-modal clues and label-level fusion

In this paper, we propose a multi-task learning (MTL) network based on the label-level fusion of metadata and hand-crafted features by unsupervised clustering to generate new clustering labels as an optimization goal. We propose a MTL module (MTLM) that incorporates an attention mechanism to enable the model to learn more integrated, variable information. We propose a dynamic strategy to adjust the loss weights of different tasks, and trade off the contributions of multiple branches. Instead of feature-level fusion, we propose label-level fusion and combine the results of our proposed MTLM with the results of the image classification network to achieve better lesion prediction on multiple dermatological datasets. We verify the effectiveness of the proposed model by quantitative and qualitative measures. The MTL network using multi-modal clues and label-level fusion can yield the significant performance improvement for skin lesion classification.

Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic

Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the nutrient concentration of Kongsfjorden change from the estuary to the interior of the fjord. Our objective was to explore the changes in bacterial community structure and metabolism-related genes from the estuary to fjord by metagenomic analysis. Our data indicate that glacial meltwater input has altered the physicochemical properties of the fjords, with a significant effect, in particular, on fjords salinity, thus altering the relative abundance of some specific bacterial groups. In addition, we suggest that the salinity of a fjord is an important factor affecting the abundance of genes associated with the nitrogen and sulfur cycles in the fjord. Changes in salinity may affect the relative abundance of microbial populations that carry metabolic genes, thus affecting the relative abundance of genes associated with the nitrogen and sulfur cycles.

Heterochronic shift in gene expression leads to ontogenetic morphological divergence between two closely related polyploid species

Heterochrony-alteration to the rate or timing of development-is an important mechanism of trait differentiation associated with speciation. Heterochrony may explain the morphological divergence between two polyploid species, June sucker (Chasmistes liorus) and Utah sucker (Catostomus ardens). The larvae of both species have terminal mouths; however, as adults, June sucker and Utah sucker develop subterminal and ventral mouths, respectively. We document a difference in the timing of shape development and a corresponding change in the timing of gene expression, suggesting the distinctive mouth morphology in June suckers may result from paedomorphosis. Specifically, adult June suckers exhibit an intermediate mouth morphology between the larval (terminal) and ancestral (ventral) states. Endemic and sympatric Chasmistes/Catostomus pairs in two other lakes also are morphologically divergent, but genetically similar. These species pairs could have resulted from the differential expression of genes and corresponding divergence in trait development. Paedomorphosis may lead to adaptive diversification in Catostomids.

Accurately clustering biological sequences in linear time by relatedness sorting

Clustering biological sequences into similar groups is an increasingly important task as the number of available sequences continues to grow exponentially. Search-based approaches to clustering scale super-linearly with the number of input sequences, making it impractical to cluster very large sets of sequences. Approaches to clustering sequences in linear time currently lack the accuracy of super-linear approaches. Here, I set out to develop and characterize a strategy for clustering with linear time complexity that retains the accuracy of less scalable approaches. The resulting algorithm, named Clusterize, sorts sequences by relatedness to linearize the clustering problem. Clusterize produces clusters with accuracy rivaling popular programs (CD-HIT, MMseqs2, and UCLUST) but exhibits linear asymptotic scalability. Clusterize generates higher accuracy and oftentimes much larger clusters than Linclust, a fast linear time clustering algorithm. I demonstrate the utility of Clusterize by accurately solving different clustering problems involving millions of nucleotide or protein sequences.

Comparative analysis of hydrogen production and bacterial communities in mesophilic and thermophilic consortia using multiple inoculum sources

This study investigates the hydrogen (H2) production performance and bacterial communities in mesophilic (37 °C) and thermophilic (50 °C) H2-producing consortia derived from different inoculum sources and utilizing food waste as a substrate. This study found notable variations in H2 production characteristics among these consortia. Among the mesophilic consortia (MC), the W-MC obtained with wetland (W) as the inoculum source exhibited the highest hydrogen production (3900 mL·L-1 and 117 mL·L-1·h-1), while among the thermophilic consortia (TC), the FP-TC obtained with forest puddle sediment (FP) as the inoculum source showed the highest performance (2112 mL·L-1 and 127 mL·L-1·h-1). This study reveals that the choice of inoculum source plays a crucial role in determining hydrogen production efficiency. Furthermore, the bacterial community analysis demonstrated varying microbial diversity and richness in different inoculum sources. Clostridium, a well-known H2-producing bacterium, was found in both mesophilic and thermophilic consortia and showed a positive correlation with H2 production. Other bacteria, such as Sporanaerobacter, Caproiciproducens, and Caldibacillus, also exhibited significant correlations with H2 production, suggesting their potential roles in the process. The study highlights the complex interactions between bacterial communities and hydrogen production performance, shedding light on the critical factors influencing this renewable energy source. Overall, this study contributes to our understanding of the microbial ecology and the factors affecting hydrogen production in different temperature conditions, which can have practical implications for optimizing biohydrogen production processes using organic waste substrates.

A 6-month exercise intervention clinical trial in women: effects of physical activity on multi-omics biomarkers and health during the first wave of COVID-19 in Korea

BACKGROUND

Coronavirus disease 2019 (COVID-19) was first reported in December 2019 and the first case in Korea was confirmed on January 20, 2020. Due to the absence of therapeutic agents and vaccines, the Korean government implemented social distancing on February 29, 2020. This study aimed to examine the effect of physical activity (PA) on health through changes in multi-omics biomarkers with a 6-month of exercise intervention during the first wave of COVID-19 in Korea.

METHODS

Twenty-seven healthy middle-aged women were recruited and 14 subjects completed the exercise intervention. The mean age (± SD) was 46.3 (± 5.33) and the mean BMI (± SD) was 24.9 (± 3.88). A total of three blood and stool samples were collected at enrollment, after period 1, and after period 2 (3-month intervals). The amount of PA was measured with an accelerometer and by questionnaire. Clinical variables were used, including blood pressure, grip strength, flexibility, and blood glucose levels and lipid markers obtained from laboratory tests. The concentration of blood metabolites was measured by targeted metabolomics. Fecal microbiome data were obtained by 16 S rRNA gene amplicon sequencing.

RESULTS

During the second half period (period 2), Coronavirus disease 2019 occurred and spread out in Korea, and PA decreased compared with the first half period (period 1) (185.9 ± 168.73 min/week to 102.5 ± 82.30 min/week; p = 0.0101). Blood pressure, hemoglobin A1c (HbA1c), and low-density lipoprotein cholesterol (LDL-C) decreased in period 1 (p < 0.05) and tended to increase again during period 2 (p < 0.05). Forty metabolites were changed significantly during period 1 (FDR p < 0.05), and we found that 6 of them were correlated with changes in blood pressure, HbA1c, and LDL-C via network analysis.

CONCLUSIONS

Our results may suggest that exercise improves health through changes in biomarkers at multi-omics levels. However, reduced PA due to COVID-19 can adversely affect health, emphasizing the necessity for sustained exercise and support for home-based fitness to maintain health.

TRIAL REGISTRATION

The trial is retrospectively registered on ClinicalTrials.gov (NCT05927675; June 30, 2023).

Microplastics in the insular marine environment of the Southwest Indian Ocean carry a microbiome including antimicrobial resistant (AMR) bacteria: A case study from Reunion Island

The increasing threats to ecosystems and humans from marine plastic pollution require a comprehensive assessment. We present a plastisphere case study from Reunion Island, a remote oceanic island located in the Southwest Indian Ocean, polluted by plastics. We characterized the plastic pollution on the island's coastal waters, described the associated microbiome, explored viable bacterial flora and the presence of antimicrobial resistant (AMR) bacteria. Reunion Island faces plastic pollution with up to 10,000 items/km2 in coastal water. These plastics host microbiomes dominated by Proteobacteria (80 %), including dominant genera such as Psychrobacter, Photobacterium, Pseudoalteromonas and Vibrio. Culturable microbiomes reach 107 CFU/g of microplastics, with dominance of Exiguobacterium and Pseudomonas. Plastics also carry AMR bacteria including β-lactam resistance. Thus, Southwest Indian Ocean islands are facing serious plastic pollution. This pollution requires vigilant monitoring as it harbors a plastisphere including AMR, that threatens pristine ecosystems and potentially human health through the marine food chain.

Role of Probiotics in Preventing Carbapenem-Resistant Enterobacteriaceae Colonization in the Intensive Care Unit: Risk Factors and Microbiome Analysis Study

Older patients with multiple comorbidities often necessitate prolonged hospital stays and antibiotic treatment in the intensive care unit (ICU), leading to a rise in multidrug-resistant organisms like carbapenem-resistant Enterobacteriaceae (CRE). This study examined risk factors for carbapenem-resistant Enterobacteriaceae colonization in the ICU and assessed probiotics' preventive role. In this single-center, retrospective study, 9099 ICU patients were tested for stool CRE culture from March 2017 to April 2022. We excluded 136 patients with CRE colonization within one week post-admission and 26 who received probiotics before CRE colonization. Ultimately, 8937 CRE-negative patients were selected. Logistic analysis identified CRE colonization risk factors and evaluated probiotics' influence, including Saccharomyces boulardii or Lactobacillus rhamnosus, used by 474 patients (5.3%) in the ICU. Compared with data on initial admission, 157 patients (1.7%) had newly discovered CRE colonization before discharge. In a multivariate analysis, coronavirus disease 2019, the ICU, tube feeding, antibiotics such as aminoglycoside, extended-spectrum penicillin, stool vancomycin-resistance enterococci colonization, and chronic kidney disease were significantly associated with de novo CRE infection. However, probiotic use was negatively correlated with CRE infection. Managing risk factors and administering probiotics in the ICU may help prevent CRE colonization; large randomized prospective studies are needed.

Gut microbiota of Suncus murinus, a naturally obesity-resistant animal, improves the ecological diversity of the gut microbiota in high-fat-diet-induced obese mice

BACKGROUND

The global population of obese individuals is increasing, affecting human health. High-fat diets are a leading cause of this epidemic, and animal models, such as mice, are often used in related research. Obese individuals have a different gut microbiota composition from non-obese ones, characterized by a sizeable population of certain bacteria associated with fat storage. The gut microbiome plays a significant role in regulating human physiological and metabolic functions. Links between obesity, high-fat diets and gut microbiota have become hot topics of discussion. Recently, research on the modulation of the gut microbiota has focused on fecal microbiota transplantation (FMT), which has been recognized as an effective method of studying the function of gut microbiota.

OBJECTIVES

The purpose of this study was to investigate how the gut microbiota of Suncus murinus, a naturally obesity-resistant animal, through FMT, affected the ecology of the gut microbiota of high-fat diet induced obese mice.

METHODS

In this study, Suncus murinus was used as a donor for FMT. High-fat diet induced C57BL/6NCrSIc mice were used as recipients, the body weight changes were measured and changes in their gut flora were analyzed using a 16S rRNA gene analysis.

RESULTS

The study found that, after the FMT procedure, the FMT group tended to have a lower body weight than the control group. At the phylum level, the most predominant phyla in all groups were Firmicutes and Proteobacteria, while Deferribacteres was not detected in the FMT or antibiotic administration groups, and Bacteroidetes was not present in the antibiotic administration group. At the genus level, the FMT group had significantly lower OTU richness than the control group but greater diversity than the control group.

CONCLUSIONS

These results indicate that FMT from Suncus murinus can help reorganize and improve the gut microbiota of mice in a balanced and diverse ecosystem.

Compositional changes in fecal microbiota in a new Parkinson's disease model: C57BL/6-Tg(NSE-haSyn) mice

BACKGROUND

The gut-brain axis (GBA) in Parkinson's disease (PD) has only been investigated in limited mice models despite dysbiosis of the gut microbiota being considered one of the major treatment targets for neurodegenerative disease. Therefore, this study examined the compositional changes of fecal microbiota in novel transgenic (Tg) mice overexpressing human α-synuclein (hαSyn) proteins under the neuron-specific enolase (NSE) to analyze the potential as GBA model.

RESULTS

The expression level of the αSyn proteins was significantly higher in the substantia nigra and striatum of NSE-hαSyn Tg mice than the Non-Tg mice, while those of tyrosine hydroxylase (TH) were decreased in the same group. In addition, a decrease of 72.7% in the fall times and a 3.8-fold increase in the fall number was detected in NSE-hαSyn Tg mice. The villus thickness and crypt length on the histological structure of the gastrointestinal (GI) tract decreased in NSE-hαSyn Tg mice. Furthermore, the NSE-hαSyn Tg mice exhibited a significant increase in 11 genera, including Scatolibacter, Clostridium, Feifania, Lachnoclostridium, and Acetatifactor population, and a decrease in only two genera in Ligilactobacillus and Sangeribacter population during enhancement of microbiota richness and diversity.

CONCLUSIONS

The motor coordination and balance dysfunction of NSE-hαSyn Tg mice may be associated with compositional changes in gut microbiota. In addition, these mice have potential as a GBA model.

Karst spring microbiome: Diversity, core taxa, and community response to pathogens and antibiotic resistance gene contamination

Karst aquifers are important water resources for drinking water supplies worldwide. Although they are susceptible to anthropogenic contamination due to their high permeability, there is a lack of detailed knowledge on the stable core microbiome and how contamination may affect these communities. In this study, eight karst springs (distributed across three different regions in Romania) were sampled seasonally for one year. The core microbiota was analysed by 16S rRNA gene amplicon sequencing. To identify bacteria carrying antibiotic resistance genes and mobile genetic elements, an innovative method was applied, consisting of high-throughput antibiotic resistance gene quantification performed on potential pathogen colonies cultivated on Compact Dry™ plates. A taxonomically stable bacterial community consisting of Pseudomonadota, Bacteroidota, and Actinomycetota was revealed. Core analysis reaffirmed these results and revealed primarily freshwater-dwelling, psychrophilic/psychrotolerant species affiliated to Rhodoferax, Flavobacterium, and Pseudomonas genera. Both sequencing and cultivation methods indicated that more than half of the springs were contaminated with faecal bacteria and pathogens. These samples contained high levels of sulfonamide, macrolide, lincosamide and streptogramins B, and trimethoprim resistance genes spread primarily by transposase and insertion sequences. Differential abundance analysis found Synergistota, Mycoplasmatota, and Chlamydiota as suitable candidates for pollution monitoring in karst springs. This is the first study highlighting the applicability of a combined approach based on high-throughput SmartChip™ antibiotic resistance gene quantification and Compact Dry™ pathogen cultivation for estimating microbial contaminants in karst springs and other challenging low biomass environments.

Automatic Clustering of Excited-State Trajectories: Application to Photoexcited Dynamics

We introduce automatic clustering as a computationally efficient tool for classifying and interpreting trajectories from simulations of photo-excited dynamics. Trajectories are treated as time-series data, with the features for clustering selected by variance mapping of normalized data. The L2-norm and dynamic time warping are proposed as suitable similarity measures for calculating the distance matrices, and these are clustered using the unsupervised density-based DBSCAN algorithm. The silhouette coefficient and the number of trajectories classified as noise are used as quality measures for the clustering. The ability of clustering to provide rapid overview of large and complex trajectory data sets, and its utility for extracting chemical and physical insight, is demonstrated on trajectories corresponding to the photochemical ring-opening reaction of 1,3-cyclohexadiene, noting that the clustering can be used to generate reduced dimensionality representations in an unbiased manner.

Contrasting Marine Microbial Communities of the Fram Strait with the First Confirmed Record of Cyanobacteria Prochlorococcus marinus in the Arctic Region

The seawater microbiome is crucial in marine ecosystems because of its role in food chains and biogeochemical cycles; thus, we studied the composition of the pelagic marine microbiome collected in the upper 50 m on the opposite sides of Fram Strait: Spitsbergen and Greenland shelves. We found out that it differed significantly, with salinity being the main environmental variable responsible for these differences. The Spitsbergen shelf was dominated by Atlantic Waters, with a rather homogenous water column in terms of salinity and temperature down to 300 m; hence, the marine microbial community was also homogenous at all sampled depths (0, 25, 50 m). On the contrary, stations on the Greenland shelf were exposed to different water masses of both Arctic and Atlantic origin, which resulted in a more diverse microbial community there. Unexpectedly, for the very first time, we identified cyanobacterium Prochlorococcus marinus in Arctic waters (Spitsbergen shelf, 75-77° N). Till now, the distribution of this cyanobacteria in oceans has been described only between 40° N and 40° S. Considering the accelerated rate of climate warming in the Arctic, our results indicated that the seawater microbiome can be viewed as an amplifier of global change and that the Atlantification is in progress.

Analysis of cnidarian Gcm suggests a neuronal origin of glial EAAT1 function

In bilaterian central nervous systems, coordination of neurotransmission by glial cells enables highly sophisticated neural functions. The diversity of transcription factors (TFs) involved in gliogenesis suggests multiple evolutionary origins of various glial cell types of bilaterians. Many of these TFs including the glial cells missing (Gcm) are also present in genomes of Cnidaria, the closest outgroup to Bilateria, but their function remains to be elucidated. In this study, we analyzed the function of Gcm, a multifunctional TF involved in development of glial and non-glial cell types, in the sea anemone, Nematostella vectensis. siRNA-mediated knockdown of Nematostella Gcm altered expression of cell adhesion proteins, glutamate and GABA transporters, ion channels, metabolic enzymes, and zinc finger and Ets-related TFs. NvGcm and mRNAs of downstream genes are expressed in broad neural cell clusters. However, immunostaining of a NvGcm target protein, the glutamate transporter, NvEAAT1, visualized a novel class of cells with flat cell bodies and no clear processes. Together with the finding of unique morphological features of NvEAAT1-functioning cells, these data suggest that extracellular glutamate metabolism, one of major glial functions, is deployed downstream of Gcm in specific neural cell types in Cnidaria.

Effects of Italian ryegrass silage-based total mixed ration on rumen fermentation, growth performance, blood metabolites, and bacterial communities of growing Hanwoo heifers

This study utilized Italian ryegrass silage (IRGS) - based total mixed ration (TMR) as feedstuff and evaluated its effects on rumen fermentation, growth performance, blood parameters, and bacterial community in growing Hanwoo heifers. Twenty-seven Hanwoo heifers (body weight [BW], 225.11 ± 10.57 kg) were randomly allocated to three experimental diets. Heifers were fed 1 of 3 treatments as follows: TMR with oat, timothy, and alfalfa hay (CON), TMR with 19% of IRGS (L-IRGS), and TMR with 36% of IRGS (H-IRGS). Feeding high levels of IRGS (H-IRGS) and CON TMR to heifers resulted in a greater molar proportion of propionate in the rumen. The impact of different TMR diets on the BW, average daily gain, dry matter intake, and feed conversion ratio of Hanwoo heifers during the growing period did not differ (p > 0.05). Furthermore, the blood metabolites, total protein, albumin, aspartate aminotransferase, glucose, and total cholesterol of the heifers were not affected by the different TMR diets (p > 0.05). In terms of rumen bacterial community composition, 264 operational taxonomic units (OTUs) were observed across the three TMR diets with 240, 239, and 220 OTUs in CON, L-IRGS, and H-IRGS, respectively. IRGS-based diets increased the relative abundances of genera belonging to phylum Bacteroidetes but decreased the abundances of genus belonging to phylum Firmicutes compared with the control. Data showed that Bacteroidetes was the most dominant phylum, while Prevotella ruminicola was the dominant species across the three TMR groups. The relative abundance of Ruminococcus bromii in the rumen increased in heifers fed with high inclusion of IRGS in the TMR (H-IRGS TMR). The relative abundance of R. bromii in the rumen significantly increased when heifers were fed H-IRGS TMR while P. ruminicola increased in both L-IRGS and H-IRGS TMR groups. Results from the current study demonstrate that the inclusion of IRGS in the TMR is comparable with the TMR containing high-quality forage (CON). Thus, a high level of IRGS can be used as a replacement forage ingredient in TMR feeding and had a beneficial effect of possibly modulating the rumen bacterial community toward mainly propionate-producing microorganisms.

Marine Bacterioplankton Community Dynamics and Potentially Pathogenic Bacteria in Seawater around Jeju Island, South Korea, via Metabarcoding

Understanding marine bacterioplankton composition and distribution is necessary for improving predictions of ecosystem responses to environmental change. Here, we used 16S rRNA metabarcoding to investigate marine bacterioplankton diversity and identify potential pathogenic bacteria in seawater samples collected in March, May, September, and December 2013 from two sites near Jeju Island, South Korea. We identified 1343 operational taxonomic units (OTUs) and observed that community diversity varied between months. Alpha- and Gamma-proteobacteria were the most abundant classes, and in all months, the predominant genera were Candidatus Pelagibacter, Leisingera, and Citromicrobium. The highest number of OTUs was observed in September, and Vibrio (7.80%), Pseudoalteromonas (6.53%), and Citromicrobium (6.16%) showed higher relative abundances or were detected only in this month. Water temperature and salinity significantly affected bacterial distribution, and these conditions, characteristic of September, were adverse for Aestuariibacter but favored Citromicrobium. Potentially pathogenic bacteria, among which Vibrio (28 OTUs) and Pseudoalteromonas (six OTUs) were the most abundant in September, were detected in 49 OTUs, and their abundances were significantly correlated with water temperature, increasing rapidly in September, the warmest month. These findings suggest that monthly temperature and salinity variations affect marine bacterioplankton diversity and potential pathogen abundance.

Comparison of Methods for Biological Sequence Clustering

Recent advances in sequencing technology have considerably promoted genomics research by providing high-throughput sequencing economically. This great advancement has resulted in a huge amount of sequencing data. Clustering analysis is powerful to study and probe the large-scale sequence data. A number of available clustering methods have been developed in the last decade. Despite numerous comparison studies being published, we noticed that they have two main limitations: only traditional alignment-based clustering methods are compared and the evaluation metrics heavily rely on labeled sequence data. In this study, we present a comprehensive benchmark study for sequence clustering methods. Specifically, i) alignment-based clustering algorithms including classical (e.g., CD-HIT, UCLUST, VSEARCH) and recently proposed methods (e.g., MMseq2, Linclust, edClust) are assessed; ii) two alignment-free methods (e.g., LZW-Kernel and Mash) are included to compare with alignment-based methods; and iii) different evaluation measures based on the true labels (supervised metrics) and the input data itself (unsupervised metrics) are applied to quantify their clustering results. The aims of this study are to help biological analyzers in choosing one reasonable clustering algorithm for processing their collected sequences, and furthermore, motivate algorithm designers to develop more efficient sequence clustering approaches.

Effect of short-term consumption of yellow peas as noodles on the intestinal environment: A single-armed pre-post comparative pilot study

Legumes contain dietary fiber and resistant starch, which are beneficial to the intestinal environment. Here, we investigated the effects of yellow pea noodle consumption on the gut microbiota and fecal metabolome of healthy individuals. This single-armed pre-post comparative pilot study evaluated eight healthy female participants who consumed yellow pea noodles for 4 weeks. The gut microbiota composition and fecal metabolomic profile of each participant were evaluated before (2 weeks), during (4 weeks), and after (4 weeks) daily yellow pea noodle consumption. 16S rRNA gene sequencing was performed on stool samples, followed by clustering of operational taxonomic units using the Cluster Database at High Identity with Tolerance and integrated QIIME pipeline to elucidate the gut microbiota composition. The fecal metabolites were analyzed using capillary electrophoresis time-of-flight mass spectrometry and liquid chromatography time-of-flight mass spectrometry. Compared to day 0, the relative abundances of five bacterial genera (Bacteroides, Bilophila, Hungatella, Parabacteroides, and Streptococcus) in the intestinal microbiota significantly decreased, wherein those of Bifidobacterium longum and Ruminococcus bromii were increased on day 29 and decreased to the basal level (day 0) on day 57. Fecal metabolomic analysis identified 11 compounds showing significant fluctuations in participants on day 29 compared to day 0. Although the average levels of short-chain fatty acids in participants did not differ significantly on day 29 compared to those on day 0, the levels tended to increase in individual participants with >8% relative abundance of R. bromii in their gut microbiota. In conclusion, incorporating yellow peas as a daily staple may confer human health benefits by favorably altering the intestinal environment.

Genome analysis of a coral-associated bacterial consortium highlights complementary hydrocarbon degradation ability and other beneficial mechanisms for the host

Here we report the oil degradation genetic potential of six oil-degrading bacteria (ODB), previously used as a bioremediation consortium, isolated from the hydrocoral Millepora alcicornis and seawater. The strains were identified as Halomonas sp. (LC_1), Cobetia sp. (LC_6), Pseudoalteromonas shioyasakiensis (LC_2), Halopseudomonas aestusnigri (LC_3), Shewanella algae (LC_4), and Brucella intermedia (LC_5). The taxonomic identification differed from that of the original paper when we used whole genome gene markers instead of just 16S rRNA gene. Genes responsible for the degradation of aromatic hydrocarbons and n-alkanes were found in all genomes, although different (and complementary) steps of the metabolic pathways were unique to each strain. Genes for naphthalene and toluene degradation were found in various strains. We annotated quinate degradation genes in LC_6, while LC_3 and LC_5 presented genes for biosurfactant and rhamnolipid biosynthesis. We also annotated genes related to beneficial mechanisms for corals, such as genes involved in nitrogen and DMSP metabolism, cobalamin biosynthesis and antimicrobial compounds production. Our findings reinforce the importance of using bacterial consortia for bioremediation approaches instead of single strains, due to their complementary genomic arsenals. We also propose a genome-based framework to select complementary ODB that can provide additional benefits to coral health.

Comparison of the Strengths and Weaknesses of Machine Learning Algorithms and Feature Selection on KEGG Database Microbial Gene Pathway Annotation and Its Effects on Reconstructed Network Topology

The development of tools for the annotation of genes from newly sequenced species has not evolved much from homologous alignment to prior annotated species. While the quality of gene annotations continues to decline as we sequence and assemble more evolutionary distant gut microbiome species, machine learning presents a high quality alternative to traditional techniques. In this study, we investigate the relative performance of common classical and nonclassical machine learning algorithms in the problem of gene annotation using human microbiome-associated species genes from the KEGG database. The majority of the ensemble, clustering, and deep learning algorithms that we investigated showed higher prediction accuracy than CD-Hit in predicting partial KEGG function. Motif-based, machine-learning methods of annotation in new species were faster and had higher precision-recall than methods of homologous alignment or orthologous gene clustering. Gradient boosted ensemble methods and neural networks also predicted higher connectivity in reconstructed KEGG pathways, finding twice as many new pathway interactions than blast alignment. The use of motif-based, machine-learning algorithms in annotation software will allow researchers to develop powerful tools to interact with bacterial microbiomes in ways previously unachievable through homologous sequence alignment alone.

Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean

Pollution in human-made fishing ports caused by petroleum from boats, dead fish, toxic chemicals, and effluent poses a challenge to the organisms in seawater. To decipher the impact of pollution on the microbiome, we collected surface water from a fishing port and a nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean. By employing 16S rRNA gene amplicon sequencing and whole-genome shotgun sequencing, we discovered that Rhodobacteraceae, Vibrionaceae, and Oceanospirillaceae emerged as the dominant species in the fishing port, where we found many genes harboring the functions of antibiotic resistance (ansamycin, nitroimidazole, and aminocoumarin), metal tolerance (copper, chromium, iron and multimetal), virulence factors (chemotaxis, flagella, T3SS1), carbohydrate metabolism (biofilm formation and remodeling of bacterial cell walls), nitrogen metabolism (denitrification, N2 fixation, and ammonium assimilation), and ABC transporters (phosphate, lipopolysaccharide, and branched-chain amino acids). The dominant bacteria at the nearby offshore island (Alteromonadaceae, Cryomorphaceae, Flavobacteriaceae, Litoricolaceae, and Rhodobacteraceae) were partly similar to those in the South China Sea and the East China Sea. Furthermore, we inferred that the microbial community network of the cooccurrence of dominant bacteria on the offshore island was connected to dominant bacteria in the fishing port by mutual exclusion. By examining the assembled microbial genomes collected from the coastal seawater of the fishing port, we revealed four genomic islands containing large gene-containing sequences, including phage integrase, DNA invertase, restriction enzyme, DNA gyrase inhibitor, and antitoxin HigA-1. In this study, we provided clues for the possibility of genomic islands as the units of horizontal transfer and as the tools of microbes for facilitating adaptation in a human-made port environment.

gUMI-BEAR, a modular, unsupervised population barcoding method to track variants and evolution at high resolution

Cellular lineage tracking provides a means to observe population makeup at the clonal level, allowing exploration of heterogeneity, evolutionary and developmental processes and individual clones' relative fitness. It has thus contributed significantly to understanding microbial evolution, organ differentiation and cancer heterogeneity, among others. Its use, however, is limited because existing methods are highly specific, expensive, labour-intensive, and, critically, do not allow the repetition of experiments. To address these issues, we developed gUMI-BEAR (genomic Unique Molecular Identifier Barcoded Enriched Associated Regions), a modular, cost-effective method for tracking populations at high resolution. We first demonstrate the system's application and resolution by applying it to track tens of thousands of Saccharomyces cerevisiae lineages growing together under varying environmental conditions applied across multiple generations, revealing fitness differences and lineage-specific adaptations. Then, we demonstrate how gUMI-BEAR can be used to perform parallel screening of a huge number of randomly generated variants of the Hsp82 gene. We further show how our method allows isolation of variants, even if their frequency in the population is low, thus enabling unsupervised identification of modifications that lead to a behaviour of interest.

RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches

We present RabbitTClust, a fast and memory-efficient genome clustering tool based on sketch-based distance estimation. Our approach enables efficient processing of large-scale datasets by combining dimensionality reduction techniques with streaming and parallelization on modern multi-core platforms. 113,674 complete bacterial genome sequences from RefSeq, 455 GB in FASTA format, can be clustered within less than 6 min and 1,009,738 GenBank assembled bacterial genomes, 4.0 TB in FASTA format, within only 34 min on a 128-core workstation. Our results further identify 1269 redundant genomes, with identical nucleotide content, in the RefSeq bacterial genomes database.

Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis

The collection of whole microbial communities (bacteria, archaea, fungi, and viruses) together constitutes the gut microbiome. Diet, age, stress, host genetics, and diseases cause increases or decreases in the relative abundance and diversity of bacterial species (dysbiosis). We aimed to investigate the gut microbial composition at different taxonomic levels of healthy controls (HCs) with active Crohn's disease (CD), ulcerative colitis (UC), and ischemic colitis (IC) using culture- and non-culture-based approaches and identify biomarkers to discriminate CD, UC, or IC. We determined the specific changes in the gut microbial profile using culture-independent (16S rRNA gene amplicon sequencing) as well as culture-based (culturomic) approaches. Biomarkers were validated using quantitative Real-Time PCR (qPCR). In both methods, bacterial diversity and species richness decreased in disease-associated conditions compared with that in HCs. Highly reduced abundance of Faecalibacterium prausnitzii and Prevotella sp. and an increased abundance of potentially pathogenic bacteria such as Enterococcus faecium, Enterococcus faecalis, and Escherichia coli in all CD, UC, or IC conditions were observed. We noted a high abundance of Latilactobacillus sakei in CD patients; Ligilactobacillus ruminis in UC patients; and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC patients. Highly reduced abundance of Faecalibacterium prausnitzii in all cases, and increased abundance of Latilactobacillus sakei and Enterococcus faecium in CD, Ligilactobacillus ruminis and Enterococcus faecium in UC, and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC could be biomarkers for CD, UC, and IC, respectively. These biomarkers may help in IBD (CD or UC) and IC diagnosis.

Fecal microbiota transplantation from Suncus murinus, an obesity-resistant animal, to C57BL/6NCrSIc mice, and the antibiotic effects in the approach

Introduction

Important studies on the relationship of the intestinal microbial flora with obesity have uncovered profound changes in the composition of the gut microbiota in obese individuals. Animal studies successfully altered body phenotypes by fecal microbiota transplantation (FMT).

Methods

In this study, we analyzed the gut microbiome of Suncus murinus (S. murinus), a naturally obesity-resistant animal, and the changes of the gut flora of C57BL/6NCrSIc mice that received gut bacteria transplantation from S. murinus by 16S rRNA gene analysis method. And analyzed and discussed the possible impact of the use of antibiotics before transplantation on the outcome of transplantation.

Results

Our results showed no significant changes in body weight in the FMT group compared to the control (AB) group, but large fluctuations due to antibiotics. There was no change in blood lipid levels between groups before and after FMT. The gut microbiota of S. murinus were enriched in Firmicutes and Proteobacteria, while Bacteroidetes were not detected, and fewer OTUs were detected in the intestine gut in comparison to other mouse groups. Statistically significant differences in alpha diversity were observed between the FMT group and other groups. Furthermore, a beta diversity analysis indicated an apparent structural separation between the FMT group and other groups.

Conclusion

It was suggested that the gut flora of S. murinus was not well established in the gut trace of mice through FMT, and the administration of antibiotics before transplantation was an important factor affecting the overall composition of the gut flora. Although FMT of S. murinus failed to completely colonize the intestinal tract of the mice, it still had a certain effect on the establishment of the intestinal flora of the mice. The unpredictable effects of pre-transplantation antibiotics on the results of transplantation cannot be ignored.

Dietary supplementation of solubles from shredded, steam-exploded pine particles modifies gut length and cecum microbiota in cyclic heat-stressed broilers

This study was conducted to investigate the effect of supplementing solubles from steam-exploded pine particles (SSPP) on mitigating the adverse effects of cyclic heat stress (CHS) in broilers which were distributed into 3 dietary treatment groups and 2 temperature conditions. Heat stress (HS) exposure for 6 h daily for 7 d adversely affected performance parameters and rectal temperature of chickens. The absolute and relative weights of the liver and bursa of Fabricius decreased in the CHS group while the relative lengths of the jejunum and ileum increased, which was rescued by dietary supplementation with SSPP. The expression of mucin2 (MUC2) and occludin (OCLN) genes was decreased in CHS birds. The expression of heat shock protein -70 and -90 increased in 0% HS compared to that in 0% NT. Birds supplemented with 0.4% SSPP had higher NADPH oxidase -1 expression than birds in the 0% and 0.1% SSPP treatments. Beta diversity of gut microbiota evaluated through unweighted UniFrac distances was significantly different among treatments. Bacteroidetes was among the 2 most abundant phyla in the cecum, which decreased with 0.1% NT and increased with 0.1% HS in comparison to 0% NT. A total of 13 genera were modified by HS, 5 were altered by dose, and nine showed an interaction effect. In conclusion, CHS adversely affects performance and gut health which can be mitigated with dietary SSPP supplementation that modifies the cecal microbiota in broilers.

Variations in antibiotic resistance genes and microbial community in sludges passing through biological nutrient removal and anaerobic digestion processes in municipal wastewater treatment plants

Antimicrobial resistance (AMR) represents a relentless, silent pandemic. Contributing to this are wastewater treatment plants (WWTPs), a potential source of antibiotic resistance genes' (ARGs) transmission to the environment, threatening public health. The presence of ARGs in pathogenic bacteria and their release into the environment by WWTPs threatens the public health. The current study investigated changes in ARGs' abundance in biological nutrient removal (BNR) processes and anaerobic digestion (AD) reactors of two WWTPs. Also, microbial community structure, which is known to shape the distribution and abundance of ARGs, was also analyzed. The relative abundance of eight ARGs (tetX, tetA, tetM, TEM, sul1, sul2, ermB and qnrD) was quantified as ARGs' copies/16 S rRNA gene copies using quantitative polymerase chain reaction (qPCR). Microbial community composition was assessed by 16 S rRNA microbiome sequencing analysis. TetX was prevalent among the eight ARGs, followed by TEM and sul1. However, its abundance was decreased in the AD sludges compared to BNR sludges. Proteobacteria was the major bacterial phylum found in all the sludge samples, while Arcobacter, 12up and Acidovorax were the predominant genera. Acinetobacter and Flavobacterium were significantly more abundant in the BNR sludges, while 12up and Aeromonas were predominant in AD sludges. Principal component analysis (PCA) revealed a clear difference in dominant ARGs and bacteria between the sludges in the processes of BNR and AD of the two WWTPs. Clinically relevant bacterial genera, Klebsiella and Enterococcus, found in both the BNR and AD sludges, were significantly correlated with the tetX gene. Throughout this study, the relationship between microbial communities and specific ARGs was revealed, illustrating that the composition of the microbial community could play a vital role in the abundance of ARGs. These results will better inform future studies aimed at controlling the spread of ARGs and their potential hosts from WWTPs.

Discrepancies of fungi and plants in the pattern of beta-diversity with environmental gradient imply a comprehensive community assembly rule

Beta-diversity partitioning has shown that the nestedness component is developed with environmental stress in a variety of taxa. However, soil fungal community may maintain its turnover components in contrast to the development of plants' nestedness component, and the potential causes remain unclear. To investigate the process of species turnover of soil fungi along a stress gradient in the Arctic, we divided species turnover component into sub-components: βsim_hete and βsim_homo representing species turnover with and without a change in the guilds, respectively. The results indicate that fungal communities maintain their turnover components, unlike plant communities; however, their βsim_hete increased under stressful conditions. Additionally, GDM analysis showed that βsim_hete was mainly explained by stress gradient and plant nestedness, suggesting that the functionality of soil fungi was ecologically filtered by environmental stress and plant community structure. The discordant trend of beta-diversity values between plant and fungi (i.e. development of plant nestedness and maintenance of fungal turnover) is possibly not caused by different assembly rules working in parallel on the two taxa, but according to an ecological rule that reflects plant-fungal interaction.

Beehives possess their own distinct microbiomes

BACKGROUND

Honeybees use plant material to manufacture their own food. These insect pollinators visit flowers repeatedly to collect nectar and pollen, which are shared with other hive bees to produce honey and beebread. While producing these products, beehives accumulate a considerable number of microbes, including bacteria that derive from plants and different parts of the honeybees' body. Whether bacteria form similar communities amongst beehives, even if located in close proximity, is an ecologically important question that has been addressed in this study. Specific ecological factors such as the surrounding environment and the beekeeping methods used can shape the microbiome of the beehive as a whole, and eventually influence the health of the honeybees and their ecosystem.

RESULTS

We conducted 16S rRNA meta-taxonomic analysis on honey and beebread samples that were collected from 15 apiaries in the southeast of England to quantify the bacteria associated with different beehives. We observed that honeybee products carry a significant variety of bacterial groups that comprise bee commensals, environmental bacteria and symbionts and pathogens of plants and animals. Remarkably, this bacterial diversity differs not only amongst apiaries, but also between the beehives of the same apiary. In particular, the levels of the bee commensals varied significantly, and their fluctuations correlated with the presence of different environmental bacteria and various apiculture practices.

CONCLUSIONS

Our results show that every hive possesses their own distinct microbiome and that this very defined fingerprint is affected by multiple factors such as the nectar and pollen gathered from local plants, the management of the apiaries and the bacterial communities living around the beehives. Based on our findings, we suggest that the microbiome of beehives could be used as a valuable biosensor informing of the health of the honeybees and their surrounding environment.

Diversity of bacterial community in the rhizosphere and bulk soil of Artemisia annua grown in highlands of Uganda

High land areas in Uganda are suitable for the farming of Artemisia annua. However, harvested A. annua from these areas contain varying concentrations of antimalarial components. This may be attributed to variation in soil properties which affect vegetative growth characters, yield and active compounds of A. annua. Thus, bacterial composition and physiochemical properties of soil from Kabale and Kabarole high land areas where A. annua is grown were studied. The study objective was to determine the diversity of bacterial community in the rhizosphere and bulk soil of A. annua grown in highlands of Uganda. Composition of bacterial community was analyzed by amplicon sequencing of 16S rRNA genes on an Illumina Miseq platform. A total of 1,420,688 read counts was obtained and clustered into 163,493 Operational Taxonomic Units ((OTU). Kabarole highland had more OTUs (87,229) than Kabale (76,264). The phylum Proteobacteria (34.2%) was the most prevalent followed by Acidobacteria (17.3%) and Actinobacteria (15.5%). The bacteria community in the two highlands significantly differed (p <0.05) among all phyla except Proteobacteria. The main genera in bulk soil were povalibacter, brevitalea, nocardioides, stenotrophobacter, gaiella and solirubrobacter. Sphingomonas, ramlibacter paludibaculum and pseudarthrobacter were the main genera in A. annua rhizospheric soil.

Bioinformatic Analysis of Natively Paired VH:VL Antibody Repertoires for Antibody Discovery

Next-generation DNA sequencing (NGS) of human antibody repertoires has been extensively implemented to discover novel antibody drugs, to analyze B-cell developmental features, and to investigate antibody responses to infectious diseases and vaccination. Because the antibody repertoire encoded by human B cells is highly diverse, NGS analyses of antibody genes have provided a new window into understanding antibody responses for basic immunology, biopharmaceutical drug discovery, and immunotherapy. However, many antibody discovery protocols analyze the heavy and light chains separately due to the short-read nature of most NGS technologies, whereas paired heavy and light chain data are required for complete antibody characterization. Here, we describe a computational workflow to process millions of paired antibody heavy and light chain DNA sequence reads using the Illumina MiSeq 2x300 NGS platform. In this workflow, we describe raw NGS read processing and initial quality filtering, the annotation and assembly of antibody clonotypes relating to paired heavy and light chain antibody lineages, and the generation of complete heavy+light consensus sequences for the downstream cloning and expression of human antibody proteins.

Monotropastrum kirishimense (Ericaceae), a new mycoheterotrophic plant from Japan based on multifaceted evidence

Due to their reduced morphology, non-photosynthetic plants have been one of the most challenging groups to delimit to species level. The mycoheterotrophic genus Monotropastrum, with the monotypic species M. humile, has been a particularly taxonomically challenging group, owing to its highly reduced vegetative and root morphology. Using integrative species delimitation, we have focused on Japanese Monotropastrum, with a special focus on an unknown taxon with rosy pink petals and sepals. We investigated its flowering phenology, morphology, molecular identity, and associated fungi. Detailed morphological investigation has indicated that it can be distinguished from M. humile by its rosy pink tepals and sepals that are generally more numerous, elliptic, and constantly appressed to the petals throughout its flowering period, and by its obscure root balls that are unified with the surrounding soil, with root tips that hardly protrude. Based on genome-wide single-nucleotide polymorphisms, molecular data has provided clear genetic differentiation between this unknown taxon and M. humile. Monotropastrum humile and this taxon are associated with different Russula lineages, even when they are sympatric. Based on this multifaceted evidence, we describe this unknown taxon as the new species M. kirishimense. Assortative mating resulting from phenological differences has likely contributed to the persistent sympatry between these two species, with distinct mycorrhizal specificity.

Effect of Lactobacillus plantarum LMT1-48 on Body Fat in Overweight Subjects: A Randomized, Double-Blind, Placebo-Controlled Trial

BACKGROUND

We investigated whether Lactobacillus plantarum strain LMT1-48, isolated from Korean fermented foods and newborn feces, is a suitable probiotic supplement to treat overweight subjects.

METHODS

In this randomized, double-blind, placebo-controlled clinical trial, 100 volunteers with a body mass index of 25 to 30 kg/m2 were assigned randomly (1:1) to receive 2×1010 colony forming units of LMT1-48 or to a placebo treatment group. Body composition was measured by dual-energy X-ray absorptiometry, and abdominal visceral fat area (VFA) and subcutaneous fat area were measured by computed tomography scanning. Changes in body fat, VFA, anthropometric parameters, and biomarkers were compared between the two treatment groups (ClinicalTrials.gov number: NCT03759743).

RESULTS

After 12 weeks of treatment, the body weight decreased significantly from 76.6±9.4 to 75.7±9.2 kg in the LMT1-48 group but did not change in the placebo group (P=0.022 between groups). A similar pattern was found in abdominal VFA between the two groups (P=0.041). Serum insulin levels, the corresponding homeostasis model assessment of insulin resistance, and leptin levels decreased in the LMT1-48 group but increased in the placebo group (all P<0.05). Decrease in body weight and body mass index by treatment with LMT1-48 was correlated with increase in Lactobacillus levels significantly. LMT1-48 also increased Oscillibacter levels significantly, which were negatively correlated with triglyceride and alanine transaminase levels.

CONCLUSION

Administration of LMT1-48 decreased body weight, abdominal VFA, insulin resistance, and leptin levels in these subjects with overweight, suggesting its anti-obesogenic therapeutic potential.

Microcalorimetry: A Novel Application to Measure In Vitro Phage Susceptibility of Staphylococcus aureus in Human Serum

Infections involving antibiotic resistant Staphylococcus aureus (S. aureus) represent a major challenge to successful treatment. Further, although bacteriophages (phages) could be an alternative to antibiotics, there exists a lack of correlation in phage susceptibility results between conventional in vitro and in vivo assays. This discrepancy may hinder the potential implementation of bacteriophage therapy. In this study, the susceptibility of twelve S. aureus strains to three commercial phage cocktails and two single phages was assessed. These S. aureus strains (including ten clinical isolates, five of which were methicillin-resistant) were compared using four assays: the spot test, efficiency of plating (EOP), the optical density assay (all in culture media) and microcalorimetry in human serum. In the spot test, EOP and optical density assay, all cocktails and single phages lysed both methicillin susceptible and methicillin resistant S. aureus strains. However, there was an absence of phage-mediated lysis in high concentrations of human serum as measured using microcalorimetry. As this microcalorimetry-based assay more closely resembles in vivo conditions, we propose that microcalorimetry could be included as a useful addition to conventional assays, thereby facilitating more accurate predictions of the in vivo susceptibility of S. aureus to phages during phage selection for therapeutic purposes.

Sex Differences in Fecal Microbiome Composition and Function of Dromedary Camels in Saudi Arabia

The gastrointestinal microbiome plays a significant role in diet digestion and the energy production of its host. Several factors that affect the gastrointestinal microbiota composition were studied in camels. Yet, the impact of sex on the gastrointestinal bacteriome of camels remains unexplored to date. In this perspective, the fecal microbiome community composition from dromedary camels was determined in 10 male and 10 female samples using the 16S rRNA amplicon, in order to estimate if this was influenced by sex. The core microbiome in females contained 284 bacterial OTUs and one archaeal OUT, whereas in males, it contained 279 bacterial OTUs and one archaeal OTU. In females, Bacteroidetes and Spirochaetes were significantly more abundant than in male camels, whereas Lentisphaerae and Euryarchaeota were significantly abundant in males. According to Principal Coordinate Analysis and UPGMA clustering, grouping with respect to sex was observed. The functional prediction results showed differences such as energy production and conversion, and that the cell wall/membrane/envelope were enriched in female camels. The fecal microbiome of male camels was rich in amino acid, lipid transport and metabolism.

Influence of dietary n-3 long-chain fatty acids on microbial diversity and composition of sows' feces, colostrum, milk, and suckling piglets' feces

Introduction

Very little is known about the impact of n-3 long-chain fatty acids (n-3 LCFAs) on the microbiota of sows and their piglets. The aim of this study was to evaluate the effect of n-3 LCFA in sow diets on the microbiota composition of sows' feces, colostrum, and milk as well as that of piglets' feces.

Methods

Twenty-two sows were randomly assigned to either a control or an n-3 LCFA diet from service to weaning. Sows' and piglets' performance was monitored. The gestating and lactating sows' microbiomes in feces, colostrum, and milk were characterized by 16s ribosomal RNA gene sequencing. The fecal microbiome from the two lowest (>800 g) and the two highest birth weight piglets per litter was also characterized, and the LPS levels in plasma were analyzed at weaning.

Results and Discussion

n-3 LCFA increased microbiota alpha diversity in suckling piglets' and gestating sows' feces. However, no effects were observed in colostrum, milk, or lactating sows' feces. Dietary n-3 LCFA modified the microbiota composition of gestating sows' feces, milk, and suckling piglets' feces, without affecting lactating sows' feces or colostrum. In gestating sows' feces and milk, the decrease in genus Succinivibrio and the increase of Proteobacteria phylum, due to the increased genera Brenneria and Escherichia, respectively, stand out. In the feces of suckling piglets, the higher abundance of the beneficial genus Akkermansia and Bacteroides, and different species of Lactobacillus are highlighted. In addition, positive correlations for families and genera were found between lactating sows' feces and milk, milk and suckling piglets' feces, and lactating sows' feces and suckling piglets' feces. To conclude, dietary n-3 LCFA had a positive impact on the microbiome of suckling piglet's feces by increasing microbial diversity and some beneficial bacteria populations, had a few minor modifications on the microbiome of milk and gestating sows' feces and did not change the microbiome in lactating sows' feces or colostrum. Therefore, this study shows the effect of dietary n-3 LCFA on the microbiota of sows, colostrum, milk, and suckling piglets during the lactation period providing crucial information on the microbiota status at the early stages of life, which have an impact on the post-weaning.

Increasing buffering capacity enhances rumen fermentation characteristics and alters rumen microbiota composition of high-concentrate fed Hanwoo steers

The buffering capacity of buffer agents and their effects on in vitro and in vivo rumen fermentation characteristics, and bacterial composition of a high-concentrate fed Hanwoo steers were investigated in this study. Treatments were comprised of CON (no buffer added), BC0.3% (low buffering capacity, 0.3% buffer), BC0.5% (medium buffering capacity, 0.5% buffer), and BC0.9% (high buffering capacity, 0.9% buffer). Four Hanwoo steers in a 4 × 4 Latin square design were used for the in vivo trial to assess the effect of treatments. Results on in vitro experiment showed that buffering capacity, pH, and ammonia-nitrogen concentration (NH3-N) were significantly higher in BC0.9% and BC0.5% than the other treatments after 24 h incubation. Individual and total volatile fatty acids (VFA) concentration of CON were lowest compared to treatment groups. Meanwhile, in vivo experiment revealed that Bacteroidetes were dominant for all treatments followed by Firmicutes and Proteobacteria. The abundances of Barnesiella intestinihominis, Treponema porcinum, and Vibrio marisflavi were relatively highest under BC0.9%, Ruminoccocus bromii and Succiniclasticum ruminis under BC0.5%, and Bacteroides massiliensis under BC0.3%. The normalized data of relative abundance of observed OTUs' representative families have grouped the CON with BC0.3% in the same cluster, whereas BC0.5% and BC0.9% were clustered separately which indicates the effect of varying buffering capacity of buffer agents. Principal coordinate analysis (PCoA) on unweighted UniFrac distances revealed close similarity of bacterial community structures within and between treatments and control, in which BC0.9% and BC0.3% groups showed dispersed community distribution. Overall, increasing the buffering capacity by supplementation of BC0.5% and and BC0.9% buffer agents enhanced rumen fermentation characteristics and altered the rumen bacterial community, which could help prevent ruminal acidosis during a high-concentrate diet.

Dysbiosis of Fecal Microbiota in Tg2576 Mice for Alzheimer's Disease during Pathological Constipation

Tg2576 transgenic mice for Alzheimer's disease (AD) exhibited significant phenotypes for neuropathological constipation, but no research has been conducted on the association of the fecal microbiota with dysbiosis. The correlation between fecal microbiota composition and neuropathological constipation in Tg2576 mice was investigated by examining the profile of fecal microbiota and fecal microbiota transplantation (FMT) in 9-10-month-old Tg2576 mice with the AD phenotypes and constipation. Several constipation phenotypes, including stool parameters, colon length, and histopathological structures, were observed prominently in Tg2576 mice compared to the wild-type (WT) mice. The fecal microbiota of Tg2576 mice showed decreases in Bacteroidetes and increases in the Firmicutes and Proteobacteria populations at the phylum level. The FMT study showed that stool parameters, including weight, water content, and morphology, decreased remarkably in the FMT group transplanted with a fecal suspension of Tg2576 mice (TgFMT) compared to the FMT group transplanted with a fecal suspension of WT mice (WFMT). The distribution of myenteric neurons and the interstitial cells of Cajal (ICC), as well as the enteric nervous system (ENS) function, remained lower in the TgFMT group. These results suggest that the neuropathological constipation phenotypes of Tg2576 mice may be tightly linked to the dysbiosis of the fecal microbiota.

Data clustering: application and trends

Clustering has primarily been used as an analytical technique to group unlabeled data for extracting meaningful information. The fact that no clustering algorithm can solve all clustering problems has resulted in the development of several clustering algorithms with diverse applications. We review data clustering, intending to underscore recent applications in selected industrial sectors and other notable concepts. In this paper, we begin by highlighting clustering components and discussing classification terminologies. Furthermore, specific, and general applications of clustering are discussed. Notable concepts on clustering algorithms, emerging variants, measures of similarities/dissimilarities, issues surrounding clustering optimization, validation and data types are outlined. Suggestions are made to emphasize the continued interest in clustering techniques both by scholars and Industry practitioners. Key findings in this review show the size of data as a classification criterion and as data sizes for clustering become larger and varied, the determination of the optimal number of clusters will require new feature extracting methods, validation indices and clustering techniques. In addition, clustering techniques have found growing use in key industry sectors linked to the sustainable development goals such as manufacturing, transportation and logistics, energy, and healthcare, where the use of clustering is more integrated with other analytical techniques than a stand-alone clustering technique.

The microbial communities (bacteria, algae, zooplankton, and fungi) improved biofloc technology including the nitrogen-related material cycle in Litopenaeus vannamei farms

Microbes are essential in biofloc technology for controlling nitrogen levels in water. The composition and function of microorganisms with biofloc systems were reported; however, data on microorganisms other than bacteria, such as algae (which are essential in the nitrogen cycle) and zooplankton (which are bacterial and algal predators), remain limited. The microbial communities (including bacteria, algae, zooplankton, and fungi) were investigated in shrimp farms using biofloc technology. Using Illumina MiSeq sequencing, the V4 region of 18S rRNA and the V3-V4 region of 16S rRNA were utilized for the analysis of the eukaryotic and prokaryotic microbial communities. As a result, it was found that the biofloc in the shrimp farm consisted of 48.73%-73.04% eukaryotic organisms and 26.96%-51.27% prokaryotic organisms. In these shrimp farms, prokaryotic microbial communities had higher specie richness and diversity than eukaryotic microbial communities. However, the eukaryotic microbial communities were more abundant than their prokaryotic counterparts, while algae and zooplankton dominated them. It was discovered that the structures of the microbial communities in the shrimp farms seemed to depend on the effects of predation by zooplankton and other related organisms. The results provided the nitrogen cycle in biofloc systems by the algal and bacterial groups in microbial communities.

Dietary shredded steam-exploded pine particle supplementation as a strategy to mitigate chronic cyclic heat stress by modulating gut microbiota in broilers

Improving the availability of underutilized waste for the economic use of livestock feed can be important in countries where feed grain production is scarce. Modulating the gut microbiota through the fibrous content present in these wastes may help mitigate the adverse effects of heat stress (HS). Here, we investigated the effects of dietary steam-exploded pine particle (SPP), a value-added waste product, on the performance, gut health, and cecum microbiota in heat-stressed broilers. Ross 308 broilers (n = 180) at 29 days of age were distributed into three dietary treatment groups (0%, 1%, and 2% SPP) and two temperature conditions (NT: 21 °C; CHS: 31 °C) and grown for seven days. CHS, but not SPP, adversely affected performance parameters, but SPP did not interactively modulate these results. On the contrary, both differently affected other parameters. CHS resulted in increased rectal temperature, total protein in serum, and Nox4 gene expression, whereas 2% SPP increased GLP-2 and the Nox4 gene expression in the duodenum in comparison to 0% and 1% SPP. CHS significantly modified the beta-diversity of cecal microbiota while 1% SPP supplementation in diets increased the abundance of the favorable bacterial genera in chicken. Concludingly, CHS adversely affects growth performances, gut health, stress-related genes, and cecal microbiota while dietary 1% SPP may facilitate the proliferation of beneficial microorganisms in the cecum of broilers.