Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities

Mixed probiotics reduce the severity of stress-induced depressive-like behaviors

In recent years, the gut microbiome has gained significant attention in the spheres of research and public health. As a result, studies have increasingly explored the potential of probiotic dietary supplements as treatment interventions for conditions such as anxiety and depression. The present study examined the effect of mixed probiotics (Lacticaseibacillus rhamnosus and Enterococcus faecium) on inflammation, microbiome composition, and depressive-like behaviors in a macaque monkey model. The mixed probiotics effectively reduced the severity of depressive-like behaviors in macaque monkeys. Further, treatment with mixed probiotics gradually increased the abundance of beneficial bacteria in the gut, improving the balance of the gut microbiota. Additionally, macaques treated with the mixed probiotics showed decreased serum levels of inflammatory factors (P < 0.05), an increased rate of L-tryptophan metabolism (P < 0.05), and the restoration of 5-HT and 5-HTP levels (P < 0.05). Correlation analysis confirmed that Lacticaseibacillus and other beneficial bacteria exhibited a negative correlation with inflammation in the body (P < 0.05), and a positive correlation with tryptophan metabolism (P < 0.05). In conclusion, the mixed probiotics effectively restored intestinal homeostasis in macaques and enhanced tryptophan metabolism, ultimately alleviating inflammation and depressive-like behaviors.

Investigations of Fish Assemblages Using Two Methods in Three Terminal Reservoirs of the East Route of South-to-North Water Transfer Project, China

The terminal reservoirs of water transfer projects directly supply water for domestic, agricultural, and industrial applications, and the water quality of these reservoirs produce crucial effects on the achievement of project targets. Typically, fish assemblages are monitored as indicators of reservoir water quality, and can also be regulated for its improvement. In the present study, we compared traditional fish landing (TFL) and environmental DNA (eDNA) metabarcoding methods for monitoring fish assemblages in three terminal reservoirs of the East Route of the South-to-North Water Transfer Project, China. Results of TFL and eDNA showed similar assemblage structures and patterns of diversity and spatial distribution with obvious differences in fish composition across three examined reservoirs. Demersal and small fish were dominant in all reservoirs. In addition, a strong association between water transfer distance and assemblages and distribution of non-native fish was found. Our findings highlight the necessity of the fish assemblage monitoring and managing for water quality and revealed the impact of water diversion distance on the structure of fish assemblages and dispersal of alien species along the water transfer project.

Postbiotic gel relieves clinical symptoms of bacterial vaginitis by regulating the vaginal microbiota

Vaginitis is the most common disease in gynecology. Vaginal dysbiosis is a main reason of bacteria vaginitis (BV), as the disrupted microecological environment facilitates the growth of various vaginal pathogens. The most dominant bacteria in the vaginal microbiota are lactic acid bacteria, which are important for maintaining vaginal health. At present, antibiotics and other drugs are often used in clinical treatment, but there are many adverse reactions and easy to relapse, and the intervention of probiotics can help restore vaginal microbiota and alleviate BV. This study is a human clinical trial of 50 patients with bacterial vaginitis (BV). The alleviation effect of applying a postbiotic gel for one week in BV was evaluated. Changes in patients' clinical indicators of BV (properties of vaginal secretion) and the vaginal microbiota after using the postbiotic gel were monitored. Our results showed that apply the postbiotic gel improved the symptoms of BV, indicated by improvement in the abnormalities of patients' vaginal secretions. After applying the gel, the relative abundance of vaginal lactobacilli increased compared to baseline. Significant negative correlations were found between lactobacilli and potential vaginal pathogens (including Gardnerella, Prevotella, and Atopobium), as well as the abnormalities of the vaginal secretion. Overall, our results showed that applying the postbiotic gel ameliorated BV, and the symptom improvement was accompanied by significant changes in the bacterial vaginal microbiota. Our study provides valuable clinical data in managing BV.

Characterization of Vaginal Microbiota in Third Trimester Premature Rupture of Membranes Patients through 16S rDNA Sequencing

In China, premature rupture of membranes (PROM) counts as a major pregnancy complication in China and usually results into adverse pregnancy outcomes. We analysed the vagina microbiome composition using 16S rDNA V3−V4 amplicon sequencing technology, in this prospective study of 441 women in their third trimester of pregnancy. We first divided all subjects into PROM and HC (healthy control) groups, in order to investigate the correlation of vagina microbiome composition and the development of PROM. We found that seven pathogens were higher in the PROM group as compared to the HC group with statistical significance. We also split all subjects into three groups based on Lactobacillus abundance-dominant (Lactobacillus > 90%), intermediate (Lactobacillus 30−90%) and depleted (Lactobacillus < 30%) groups, and explored nine pathogenic genera that were higher in the depleted group than the intermediate and dominant groups having statistical significance. Finally, using integrated analysis and logistics regression modelling, we discovered that Lactobacillus (coeff = −0.09, p = 0.04) was linked to the decreased risk of PROM, while Gardnerella (coeff = 0.04, p = 0.02), Prevotella (coeff = 0.11, p = 0.02), Megasphaera (coeff = 0.04, p = 0.01), Ureaplasma (coeff = 0.004, p = 0.01) and Dialister (coeff = 0.001, p = 0.04) were associated with the increased risk of PROM. Further study on how these pathogens interact with vaginal microbiota and the host would result in a better understanding of PROM development.

Comparing PCR-generated artifacts of different polymerases for improved accuracy of DNA metabarcoding

Accuracy of PCR amplification is vital for obtaining reliable amplicon-sequencing results by metabarcoding. Here, we performed a comparative analysis of error profiles in the PCR products by 14 different PCR kits using a mock eukaryotic community DNA sample mimicking metabarcoding analysis. To prepare a mock eukaryotic community from the marine environment, equal amounts of plasmid DNA from 40 microalgal species were mixed and used for amplicon-sequencing by a high-throughput sequencing approach. To compare the differences in PCR kits used for this experiment, we focused on the following seven parameters: 1) Quality, 2) Chimera, 3) Blast top hit accuracy, 4) Deletion, 5) Insertion, 6) Base substitution and 7) Amplification bias amongst species. The results showed statistically significant differences (p &lt; 0.05) for all of the seven parameters depending on the PCR kits used. These differences may result from the different DNA polymerases included in each kit, although the result can also be influenced by PCR reaction conditions. Simultaneous analysis of several parameters suggested that kits containing KOD plus Neo (TOYOBO) and HotStart Taq DNA polymerase (BiONEER, CA, US) at the annealing temperature of 65 °C displayed better results in terms of parameters associated with chimeras, top hit similarity and deletions.

Biomonitoring of Fungal and Oomycete Plant Pathogens by Using Metabarcoding

Fungal and oomycete plant pathogens are responsible for the devastation of various ecosystems such as forest and crop species worldwide. In an effort to protect such natural resources for food, lumber, etc., early detection of non-indigenous phytopathogenic fungi in new areas is a key approach in managing threats at their source of introduction. A workflow was developed using high-throughput sequencing (HTS), more specifically metabarcoding, a method for rapid and higher throughput species screening near high-risk areas, and over larger geographical spaces. Biomonitoring of fungal and oomycete entities of plant pathogens (e.g., airborne spores) regained from environmental samples and their processing by metabarcoding is thoroughly described here. The amplicon-based approach goes from DNA and sequencing library preparation using custom-designed polymerase chain reaction (PCR) fusion primers that target the internal transcribed spacer 1 (ITS1) from fungi and oomycetes and extends to multiplex HTS with the Ion Torrent platform. In addition, a brief and simplified overview of the bioinformatics analysis pipeline and other available tools required to process amplicon sequences is also included. The raw data obtained and processed enable users to select a bioinformatics pipeline in order to directly perform biodiversity, presence/absence, geographical distribution, and abundance analyses through the tools suggested, which allows for accelerated identification of phytopathogens of interest.

Analyzing the human gut mycobiome – a short guide for beginners

The human body is a dynamic ecosystem consisting of millions of microbes which are often comprised under the term microbiome. Compared to bacteria, which count for the overwhelming majority of the microbiome, the number of human-associated fungi is small and often underestimated. Nonetheless, they can be found in different host niches such as the gut, the oral cavity and the skin. The fungal community has several potential roles in health and disease of the human host. In this review we will focus on intestinal fungi and their interaction with the host as well as bacteria. We also summarize technical challenges and possible biases researchers must be aware of when conducting mycobiome analysis.

Gut and Vagina Microbiota Associated With Estrus Return of Weaning Sows and Its Correlation With the Changes in Serum Metabolites

More and more studies have indicated that gut microbiota takes part in the biosynthesis and metabolism of sex hormones. Inversely, sex hormones influence the composition of gut microbiota. However, whether microbiota in the gut and vagina is associated with estrus return of weaning sows is largely unknown. Here, using 16S rRNA gene sequencing in 158 fecal and 50 vaginal samples, we reported the shifts in the gut and vaginal microbiota between normal return and non-return sows. In fecal samples, Lactobacillus and S24-7 were enriched in normal return sows, while Streptococcus luteciae, Lachnospiraceae, Clostridium, and Mogibacterium had higher abundance in non-return sows. In vaginal swabs, the operational taxonomic units (OTUs) annotated to Clostridiales, Ruminoccaceae, and Oscillospira were enriched in normal return sows, while those OTUs annotated to Campylobacter, Anaerococcus, Parvimonas, Finegoldia, and Dorea had higher abundances in non-return sows. Co-abundance group (CAG) analysis repeated the identification of the bacterial taxa associated with the estrus return of weaning sows. The predicted functional capacities in both gut and vaginal microbiome were changed between normal return and non-return sows. Serum metabolome profiles were determined by non-targeted metabolome analysis in seven normal return and six non-return sows. The metabolite features having higher abundance in normal return sows were enriched in the pathways Steroid hormone biosynthesis, Starch and sucrose metabolism, Galactose metabolism, and Vitamin B6 metabolism, while the metabolite features belonging to organic acids and derivatives, indoles and derivatives, sulfoxides, and lignans and neolignans had significantly higher abundance in non-return sows. Correlation analysis found that the changes in gut microbiota were associated with the shifts of serum metabolites and suggested that certain bacteria might affect estrus return of weaning sow through serum metabolites. These findings may provide new insights for understanding the role of the gut and vaginal microbiota in sow return to estrus after weaning.

Identification of the gut microbiota biomarkers associated with heat cycle and failure to enter oestrus in gilts

Failed puberty is one of the main reasons for eliminating gilts from production herds. This is often caused by disorders of sex hormones. An increasing number of studies have suggested that the gut microbiota may regulate sex hormones and vice versa. Whether the gut microbiota is involved in the failure of oestrus in gilts remains unknown. We used 16S rRNA gene sequencing, network-based microbiota analysis and prediction of functional capacity from 16S rRNA gene sequences to explore the shifts in the gut microbiota throughout a heat cycle in 22 eight-month-old gilts. We found that a module of co-occurrence networks composed of Sphaerochaeta and Treponema, co-occurred with oestrus during a heat cycle. The mcode score of this module reflecting the stability and importance in the network achieved the highest value at the oestrus stage. We then identified bacterial biosignatures associated with the failure to show puberty in 163 gilts. Prevotella, Treponema, Faecalibacterium, Oribacterium, Succinivibrio and Anaerovibrio were enriched in gilts showing normal heat cycles, while Lachnospiraceae, Ruminococcus, Coprococcus and Oscillospira had higher abundance in gilts failing to show puberty. Prediction of functional capacity of the gut microbiome identified a lesser abundance of the pathway 'retinol metabolism' in gilts that failed to undergo puberty. This pathway was also significantly associated with those bacterial taxa involved in failed puberty identified in this study (P < 0.05). This result suggests that the changed gut bacteria might result in a disorder of retinol metabolism, and this may be an explanation for the failure to enter oestrus.

Molecular characterization of harmful algal blooms in the Bohai Sea using metabarcoding analysis

Although the occurrences of harmful algal blooms (HABs) have been intensifying, many HABs in coastal waters may have been neglected despite their damaging impact directly on ecology and indirectly on human and animal health. The current detection of HABs depends primarily on the water coloration, chlorophyll intensity, cell density, and mortality due to HAB toxicity. Such methods may not be adequately sensitive to detecting HABs that are relatively transient or small scale. The Bohai Sea is the largest inlet of the Yellow Sea located on the northeast coast of China and famous for shipping and marine aquacultures. HABs frequently occur in the Bohai Sea. In this study, we explored the composition, diversity, and distribution of HAB species using the metabarcoding approach. Through sequencing and the analyzing the 18S rDNA V4 region of 15 samples collected from spatially isolated sites in the Bohai Sea during an expedition in the summer of 2019, we identified 74 potential HAB species including 34 that had not been reported in the Bohai Sea in previous studies. This project provided a detailed analysis of phytoplankton composition, and molecular detection of HAB species in the Bohai Sea. In particular, these analyses revealed extremely high relative abundances of the ichthyotoxic phytoplankton species Vicicitus globosus (Dictyochophyceae) at multiple adjacent sampling sites in the Bohai Bay, which were close to the Yellow River Estuary during the expedition. The results revealed the occurrence of a potential HAB event that would be otherwise undetected using conventional methods, highlighting the sensitivity and power of metabarcoding analysis in detecting HABs and HAB species. This research suggested the value for routine and long-term monitoring of HAB species as an approach for monitoring HABs.

A comprehensive metagenomics framework to characterize organisms relevant for planetary protection

BACKGROUND

Clean rooms of the Space Assembly Facility (SAF) at the Jet Propulsion Laboratory (JPL) at NASA are the final step of spacecraft cleaning and assembly before launching into space. Clean rooms have stringent methods of air-filtration and cleaning to minimize microbial contamination for exoplanetary research and minimize the risk of human pathogens, but they are not sterile. Clean rooms make a selective environment for microorganisms that tolerate such cleaning methods. Previous studies have attempted to characterize the microbial cargo through sequencing and culture-dependent protocols. However, there is not a standardized metagenomic workflow nor analysis pipeline for spaceflight hardware cleanroom samples to identify microbial contamination. Additionally, current identification methods fail to characterize and profile the risk of low-abundance microorganisms.

RESULTS

A comprehensive metagenomic framework to characterize microorganisms relevant for planetary protection in multiple cleanroom classifications (from ISO-5 to ISO-8.5) and sample types (surface, filters, and debris collected via vacuum devices) was developed. Fifty-one metagenomic samples from SAF clean rooms were sequenced and analyzed to identify microbes that could potentially survive spaceflight based on their microbial features and whether the microbes expressed any metabolic activity or growth. Additionally, an auxiliary testing was performed to determine the repeatability of our techniques and validate our analyses. We find evidence that JPL clean rooms carry microbes with attributes that may be problematic in space missions for their documented ability to withstand extreme conditions, such as psychrophilia and ability to form biofilms, spore-forming capacity, radiation resistance, and desiccation resistance. Samples from ISO-5 standard had lower microbial diversity than those conforming to ISO-6 or higher filters but still carried a measurable microbial load.

CONCLUSIONS

Although the extensive cleaning processes limit the number of microbes capable of withstanding clean room condition, it is important to quantify thresholds and detect organisms that can inform ongoing Planetary Protection goals, provide a biological baseline for assembly facilities, and guide future mission planning. Video Abstract.

Identification of Enterotype and Its Effects on Intestinal Butyrate Production in Pigs

Simple Summary

Enterotype (ET) is defined based on different gut microbial community composition. It has been considered as a critical factor strongly associated with the porcine feed efficiency and growth characteristic. However, little is known about whether the ET clustering depends on the pig breeds and the effects of the different enterotypes on the butyrate metabolism in pigs. Therefore, we studied Jinhua pig’s enterotype by using 16S rRNA high throughput sequencing, and then analyzed the interaction between enterotype and butyrate production. Results showed that we identified three ETs driven by discriminative genera dominated by Lactobacillus, Clostridium sensu stricto 1, and Bacteroides, respectively. Significant differences in the fecal contents of butyrate production and butyrate-producing bacteria were observed among ETs. These findings present a first overview of the enterotypes clustering in Jinhua pigs and provide new insights into the relationship between the different ETs and intestinal butyrate production.

Abstract

Gut microbiota is thought to play a crucial role in nutrient digestion for pigs, especially in processing indigestible polysaccharides in the diets to produce short-chain fatty acids (SCFAs). However, the link between microbiota community structure and phenotypic performances are poorly understood. In the present study, the fecal samples of 105 Jinhua pigs at 105 days of age were clustered into three enterotypes (ETs, ET1, ET2, and ET3) that are subpopulations of distinct bacterial community composition by using 16S rRNA high throughput sequencing. The α-diversity indices (the OTU number and Shannon index) were significantly different among the ETs (p < 0.001). At the genus level, the ET1 group was over-represented by Lactobacillus (17.49%) and Clostridium sensu stricto 1 (11.78%), the ET2 group was over-represented by Clostridium sensu stricto 1 (17.49%) and Bifidobacterium (11.78%), and the ET3 group was over-represented by Bacteroides (18.17%). Significant differences in the fecal contents of butyrate were observed among ETs, with the highest level detected in ET3 and the lowest in ET2 (p < 0.05). Consistently, more copies of the terminal genes for butyrate synthesis, butyrate kinase (Buk) and butyryl coenzyme A (CoA): acetate CoA transferase (But) were detected by qPCR in the fecal samples of the ET3 group as compared to other two groups (p < 0.05). In addition, of the two genes, But was demonstrated to be more relevant to the butyrate content (R = 0.7464) than Buk (R = 0.4905) by correlation analysis. In addition, based on the taxonomic analysis, we found that Faecalibacterium was the most relevant butyrate-producing genera with fecal butyrate contents in Jinhua pigs, followed by Butyricicoccus, Eubacterium, Butyricimonas, Blautia, and Anaerostipes, all of which showed significantly higher richness in ET3 than as compared to ET1 and ET2 (p < 0.05). Collectively, this work presents a first overview of the enterotypes clustering in Jinhua pigs and will help to unravel the functional implications of ETs for the pig’s phenotypic performance and nutrient metabolism.

Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach

Traditionally slurry is used as source of nitrogen, phosphorous, and potassium in bio fertilizers to improve crop production. However, poorly managed slurry causes a hazardous effect to the environment by producing greenhouse gases, causing the eutrophication of water bodies, and polluting the groundwater. It has been largely reported that the microbial presence in slurry causing a diverse effect on its storage and disposal system. However, the diversity of bacterial populations in pig slurries remains largely unexplored. Here we report the bacterial diversity present in the slurry from slurry pits, and the effect of storage time on bacterial population. We collected 42 samples from three different pig slurry pits, as three replicates from each one until the 14th week. We used the 16S rRNA, Quantitative Insights Into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) protocols for the metagenomic downstream analysis. Taxonomic annotation using the Greengenes metagenomic database indicated that on an average 76.2% Firmicutes, 14.4% Bacteroidetes, 4.9% Proteobacteria, etc. microbial populations were present. Comparative microbial analysis showed that the population of Firmicutes decreased from the first to the 14th week, whereas the population of Bacteroidetes increased from the first to the 14th week. Through principal coordinate analysis (PCoA), (linear discriminant analysis effect size (LEfSe), and Pearson's correlation analysis, we found microbial biomarkers according to the storage time point. All bacterial populations were well clustered according to the early, middle, and last weeks of storage. LEfSe showed that Actinobacteria, Lachnospiraceae, Ruminococcaceae, and Bacteroidia are dominantly present in first, seventh, ninth, and 14th week, respectively. Lachnospiraceae and Ruminococcaceae are ubiquitous gastrointestinal non-pathogenic bacteria. KEGG pathways, such as membrane transport, carbohydrate and amino acid metabolism, genetic replication and repair, were significant among all samples. Such a KEGG pathway may indicate the association between the host organism's metabolic activity and the microbes present in the gastro intestinal tract (GIT).

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

The promise and challenge of cancer microbiome research

Many microbial agents have been implicated as contributors to cancer genesis and development, and the search to identify and characterize new cancer-related organisms is ongoing. Modern developments in methodologies, especially culture-independent approaches, have accelerated and driven this research. Recent work has shed light on the multifaceted role that the community of organisms in and on the human body plays in cancer onset, development, detection, treatment, and outcome. Much remains to be discovered, however, as methodological variation and functional testing of statistical correlations need to be addressed for the field to advance.

Increased yield and CO2 sequestration potential with the C4 cereal Sorghum bicolor cultivated in basaltic rock dust-amended agricultural soil

Land-based enhanced rock weathering (ERW) is a biogeochemical carbon dioxide removal (CDR) strategy aiming to accelerate natural geological processes of carbon sequestration through application of crushed silicate rocks, such as basalt, to croplands and forested landscapes. However, the efficacy of the approach when undertaken with basalt, and its potential co-benefits for agriculture, require experimental and field evaluation. Here we report that amending a UK clay-loam agricultural soil with a high loading (10 kg/m² ) of relatively coarse-grained crushed basalt significantly increased the yield (21 ± 9.4%, SE) of the important C₄ cereal Sorghum bicolor under controlled environmental conditions, without accumulation of potentially toxic trace elements in the seeds. Yield increases resulted from the basalt treatment after 120 days without P- and K-fertilizer addition. Shoot silicon concentrations also increased significantly (26 ± 5.4%, SE), with potential benefits for crop resistance to biotic and abiotic stress. Elemental budgets indicate substantial release of base cations important for inorganic carbon removal and their accumulation mainly in the soil exchangeable pools. Geochemical reactive transport modelling, constrained by elemental budgets, indicated CO₂ sequestration rates of 2-4 t CO₂ /ha, 1-5 years after a single application of basaltic rock dust, including via newly formed soil carbonate minerals whose long-term fate requires assessment through field trials. This represents an approximately fourfold increase in carbon capture compared to control plant-soil systems without basalt. Our results build support for ERW deployment as a CDR technique compatible with spreading basalt powder on acidic loamy soils common across millions of hectares of western European and North American agriculture.

MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics

BACKGROUND

Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts, and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics.

RESULTS

MetaEuk is a toolkit for high-throughput, reference-based discovery, and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk's power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted >12,000,000 protein-coding genes in 8 days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups.

CONCLUSION

The open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation. Video abstract.

Effect of endometriosis on the fecal bacteriota composition of mice during the acute phase of lesion formation

Accumulating evidence indicates that there is an interaction between the gut microbiota and endometriotic lesions. The new formation of these lesions is associated with stem cell recruitment, angiogenesis and inflammation, which may affect the composition of the gut microbiota. To test this hypothesis, we herein induced endometriotic lesions by transplantation of uterine tissue fragments from green fluorescent protein (GFP)⁺ donor mice into the peritoneal cavity of GFP^- C57BL/6 wild-type mice. Sham-transplanted animals served as controls. Fecal pellets of the animals were collected 3 days before as well as 7 and 21 days after the induction of endometriosis to analyze the composition of the gut microbiota by means of 16S ribosomal RNA gene sequencing. The transplantation of uterine tissue fragments resulted in the establishment of endometriotic lesions in all analyzed mice. These lesions exhibited a typical histomorphology with endometrial glands surrounded by a vascularized stroma. Due to their bright GFP signal, they could be easily differentiated from the surrounding GFP^- host tissue. Bacterial 16S rRNA genes were successfully PCR-amplified from the DNA extracts of all obtained mice fecal samples. However, no significant effect of endometriosis induction on the composition of the bacterial microbiota was detected with our experimental setup. Our findings allow careful speculation that endometriosis in mice does not induce pronounced dysbiosis during the acute phase of lesion formation.

The mycobiome of Australian tree hollows in relation to the Cryptococcus gattii and C. neoformans species complexes

Cryptococcosis is a fungal infection caused by members of the Cryptococcus gattii and C. neoformans species complexes. The C. gattii species complex has a strong environmental association with eucalypt hollows (particularly Eucalyptus camaldulensis), which may present a source of infection. It remains unclear whether a specific mycobiome is required to support its environmental survival and growth. Conventional detection of environmental Cryptococcus spp. involves culture on differential media, such as Guizotia abyssinica seed agar. Next-generation sequencing (NGS)-based culture-independent identification aids in contextualising these species in the environmental mycobiome. Samples from 23 Australian tree hollows were subjected to both culture- and amplicon-based metagenomic analysis to characterize the mycobiome and assess relationships between Cryptococcus spp. and other fungal taxa. The most abundant genera detected were Coniochaeta, Aspergillus, and Penicillium, all being commonly isolated from decaying wood. There was no correlation between the presence of Cryptococcus spp. in a tree hollow and the presence of any other fungal genus. Some differences in the abundance of numerous taxa were noted in a differential heat tree comparing samples with or without Cryptococcus-NGS reads. The study expanded the known environmental niche of the C. gattii and C. neoformans species complexes in Australia with detections from a further five tree species. Discrepancies between the detection of Cryptococcus spp. using culture or NGS suggest that neither is superior per se and that, rather, these methodologies are complementary. The inherent biases of amplicon-based metagenomics require cautious interpretation of data through consideration of its biological relevance.

Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance

Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.

Host Gender and Androgen Levels Regulate Gut Bacterial Taxa in Pigs Leading to Sex-Biased Serum Metabolite Profiles

Gut microbiota regulates host metabolism and immunity. The phylogenetic composition of gut microbiota is influenced by diverse factors that include host gender. In this study, the effects of gender on gut microbial composition and its subsequent influence on serum metabolites in pigs were evaluated. The bacterial composition of feces samples was determined by 16S rRNA gene sequencing in 293 pure-bred Duroc pigs (108 gilts and 185 entire boars) and 64 validated pigs from an eight-breed mosaic F₆ population. Twenty-eight F₆ boars were castrated at 80 days of age to evaluate the effects of androgen on gut microbial composition. Untargeted serum metabolite features were determined in 45 boars and 26 gilts by an ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). The study observed an obvious influence of host gender on the gut microbial composition and identified numerous sex-biased bacterial taxa. These included Veillonellaceae, Roseburia, Bulleidia, and Escherichia which showed the higher abundance in boars, and Treponema and Bacteroides which were over-represented in gilts. Castration significantly shifted the fecal microbiota composition of the boars toward that of gilts. The predicted functional pathways of the gut microbiome related to obesity and energy harvest were enriched in gilts, and positively associated with gilt-enriched bacteria. Functional pathways related to peptidases and carbohydrate metabolism were enriched in boars and positively associated with boar-enriched bacteria. Serum metabolites related to androgen and cresol metabolism were identified as sex-biased metabolites. Correlation analysis between serum metabolites and sex-biased bacteria identified that the serum concentration of androgen-related metabolites was positively correlated with Bulleidia and Escherichia, but negatively associated with Treponema, suggesting a significant interaction between gut microbiota and host sex hormone metabolism. These results offer basic knowledge of how host gender and gut microbiota influence host metabolism.

Composition and dynamics of the bacterial communities present in the post-slaughter environment of farmed Atlantic salmon (Salmo salar L.) and correlations to gelatin degrading activity

Background

Microbial analyses performed in connection with the post-slaughter environment of farmed Atlantic salmon (Salmo salar L.) have mostly focused on specific bacteria that may have negative effects on the health of consumers. However, bacteria may also affect other quality variables. The objective of this study was to provide general knowledge about composition and dynamics of the bacterial communities present at slaughter and cold storage of farmed Atlantic salmon, as well as reveal any possible correlations to gelatinase activity, which may affect fillet quality. Thus, these data may provide a basis for optimization opportunities in the aquaculture industry.

Methods

Samples were taken from the digestive system harvested from 15 salmon immediately after slaughter. Another 17 salmon were taken from the processing line just before the final cleaning stage; of these eight were distributed in three iced storage boxes while the other nine were rinsed an extra time with industrial water before being distributed into another three storage boxes. In the following 6 days, samples were taken of skin mucus, liquids in the abdominal cavity and the storage ice. The compositions of the bacterial communities were analyzed by next-generation sequencing and gelatinase activity was measured in all samples except the storage ice.

Results

The bacterial communities in the digestive tract samples were dominated by the family Mycoplasmataceae. The genus Aliivibrio was also relatively abundant. Bacterial communities in the abdominal cavity were generally more diverse than the intestinal samples. However, all of the abdominal samples from storage box no. 3 had a high relative abundance of Mycoplasmataceae, and could not be distinguished from the intestinal samples (Q = 1.27, p = 0.633) while being significantly different from the other abdominal samples (Q = 9.02, p = 0.01). In addition, the abdominal samples from storage box no. 3 had a significantly higher gelatin degrading activity (Q = 9.43, p = 0.001) than those from the other storage boxes and similar to the high gelatinase activity in the intestinal samples. This indicated that in storage box no. 3 there was a transfer of intestinal fluids to the abdominal cavities, which was not removed by the cleaning procedure. There was a significant difference of the major phyla detected in the skin mucus of salmon rinsed an additional time, as these salmon had a higher relative amount of Firmicutes (F = 4.76, p = 0.04) and lower amount of Proteobacteria (F = 4.41, p = 0.047).

Conclusions

The study showed a correlation between intestinal fluids and bacteria left in the abdominal cavity and gelatinase activity. This suggested that intestinal fluids and/or bacteria could enhance the degradation of connective tissue in the abdominal cavity and hence negatively affect the fillet quality. In addition, the study provided general knowledge of the composition and dynamics of bacterial communities present.

Evaluating the profound effect of gut microbiome on host appetite in pigs

Background

There are growing evidences showing that gut microbiota should play an important role in host appetite and feeding behavior. However, what kind of microbe(s) and how they affect porcine appetite remain unknown.

Results

In this study, 280 commercial Duroc pigs were raised in a testing station with the circadian feeding behavior records for a continuous period of 30–100 kg. We first analyzed the influences of host gender and genetics in porcine average daily feed intake (ADFI), but no significant effect was observed. We found that the Prevotella-predominant enterotype had a higher ADFI than the Treponema enterotype-like group. Furthermore, 12 out of the 18 OTUs positively associated with the ADFI were annotated to Prevotella, and Prevotella was the hub bacteria in the co-abundance network. These results suggested that Prevotella might be a keystone bacterial taxon for increasing host feed intake. However, some bacteria producing short-chain fatty acids (SCFAs) and lactic acid (e.g. Ruminococcaceae and Lactobacillus) showed negative associations with the ADFI. Predicted function capacity analysis showed that the genes for amino acid biosynthesis had significantly different enrichment between pigs with high and low ADFI.

Conclusions

The present study provided important information on the profound effect of gut microbiota on porcine appetite and feeding behavior. This will profit us to regulate porcine appetite through modulating the gut microbiome in the pig industry.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1364-8) contains supplementary material, which is available to authorized users.

Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

Structural inflexibility of the rhizosphere microbiome in mangrove plant Kandelia obovata under elevated CO2

Rhizosphere microbial communities play an important role in mediating the decomposition of soil organic matter. Increased CO₂ concentration may increase plant growth by stimulating photosynthesis or improving water use efficiency. However, possible eco-physiological influences of this greenhouse gas in mangrove plants are not well understood, especially how rhizosphere microbial communities respond to CO₂ increase. We characterized the effect of elevated CO₂ (eCO₂) on rhizospheric microbial communities associated with the mangrove plant Kandelia candel for 20 weeks, eCO₂ increased plant chlorophyll a levels and root microbial biomass. Operational taxonomic unit analysis revealed no significant effects of eCO₂ on rhizospheric bacterial communities; however, some influence on archaeal community structure was observed, especially on the ammonia-oxidizing archaea. Principal component analysis showed that microbial biomass C, total nitrogen, C/N ratio, nitrate nitrogen, and salinity were the main factors structuring the microbial community. The relative contribution of environmental parameters to variability among samples was 31.0%. In addition, functional analysis by average well color development showed that carbon source utilization under eCO₂ occurred in the order amino acids > carbohydrates > polymers > carboxylic acids > amines > phenolic acids; whereas, sugars, amino acids, and carboxylic acids were the preferred carbon sources in control groups. Differences in utilization ability of carbohydrates and amino acids resulted in changes in carbon metabolism between the two groups. Rhizosphere microbial communities appear to have some buffering ability in response to short-term (20 weeks) CO₂ increase, during which the metabolic efficiency of carbon sources is changed. The results will help better understand the structural inflexibility and functional plasticity of the rhizosphere microbiome in mangrove plants facing a changing environment (such as global climate change).

Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach

The complicated relationships among environmental microorganisms are regulated by quorum sensing (QS). Understanding QS-based signals could shed light on the interactions between microbial communities in certain environments. Although QS characteristics have been widely discussed, few studies have been conducted on the role of QS in phycospheric microorganisms. Here, we used metagenomics to examine the profile of AI-1 (AinS, HdtS, LuxI) and AI-2 (LuxS) autoinducers from a deeply sequenced microbial database, obtained from a complete dinoflagellate bloom. A total of 3001 putative AI-1 homologs and 130 AI-2 homologs were identified. The predominant member among the AI groups was HdtS. The abundance of HdtS, AinS, and LuxS increased as the bloom developed, whereas the abundance of LuxI showed the opposite trend. Phylogenetic analysis suggested that HdtS and LuxI synthase originated mainly from alpha-, beta-, and gamma-Proteobacteria, whereas AinS synthase originated solely from Vibrionales. In comparison to AI-1, the sequences related to AI-2 (LuxS) demonstrated a much wider taxonomic coverage. Some significant correlations were found between dominant species and QS signals. In addition to the QS, we also performed parallel analysis of the quorum quenching (QQ) sequences. In comparison to QS, the relative abundance of QQ signals was lower; however, an obvious frequency correlation was observed. These results suggested that QS and QQ signals co-participate in regulating microbial communities during an algal bloom. These data helped to reveal the characteristic behavior of algal symbiotic bacteria, and facilitated a better understanding of microbial dynamics during an algal bloom event from a chemical ecological perspective.

Ecological influence of sediment bypass tunnels on macroinvertebrates in dam-fragmented rivers by DNA metabarcoding

Sediment bypass tunnels (SBTs) are guiding structures used to reduce sediment accumulation in reservoirs during high flows by transporting sediments to downstream reaches during operation. Previous studies monitoring the ecological effects of SBT operations on downstream reaches suggest a positive influence of SBTs on riverbed sediment conditions and macroinvertebrate communities based on traditional morphology-based surveys. Morphology-based macroinvertebrate assessments are costly and time-consuming, and the large number of morphologically cryptic, small-sized and undescribed species usually results in coarse taxonomic identification. Here, we used DNA metabarcoding analysis to assess the influence of SBT operations on macroinvertebrates downstream of SBT outlets by estimating species diversity and pairwise community dissimilarity between upstream and downstream locations in dam-fragmented rivers with operational SBTs in comparison to dam-fragmented (i.e., no SBTs) and free-flowing rivers (i.e., no dam). We found that macroinvertebrate community dissimilarity decreases with increasing operation time and frequency of SBTs. These factors of SBT operation influence changes in riverbed features, e.g. sediment relations, that subsequently effect the recovery of downstream macroinvertebrate communities to their respective upstream communities. Macroinvertebrate abundance using morphologically-identified specimens was positively correlated to read abundance using metabarcoding. This supports and reinforces the use of quantitative estimates for diversity analysis with metabarcoding data.

In Situ Stimulation of Thiocyanate Biodegradation through Phosphate Amendment in Gold Mine Tailings Water

Thiocyanate (SCN^-) is a contaminant requiring remediation in gold mine tailings and wastewaters globally. Seepage of SCN^--contaminated waters into aquifers can occur from unlined or structurally compromised mine tailings storage facilities. A wide variety of microorganisms are known to be capable of biodegrading SCN^-; however, little is known regarding the potential of native microbes for in situ SCN^- biodegradation, a remediation option that is less costly than engineered approaches. Here we experimentally characterize the principal biogeochemical barrier to SCN^- biodegradation for an autotrophic microbial consortium enriched from mine tailings, to arrive at an environmentally realistic assessment of in situ SCN^- biodegradation potential. Upon amendment with phosphate, the consortium completely degraded up to ∼10 mM SCN^- to ammonium and sulfate, with some evidence of nitrification of the ammonium to nitrate. Although similarly enriched in known SCN^--degrading strains of thiobacilli, this consortium differed in its source (mine tailings) and metabolism (autotrophy) from those of previous studies. Our results provide a proof of concept that phosphate limitation may be the principal barrier to in situ SCN^- biodegradation in mine tailing waters and also yield new insights into the microbial ecology of in situ SCN^- bioremediation involving autotrophic sulfur-oxidizing bacteria.

A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies

The main objective of this work was to develop and validate a robust and reliable "from-benchtop-to-desktop" metabarcoding workflow to investigate the diet of invertebrate-eaters. We applied our workflow to faecal DNA samples of an invertebrate-eating fish species. A fragment of the cytochrome c oxidase I (COI) gene was amplified by combining two minibarcoding primer sets to maximize the taxonomic coverage. Amplicons were sequenced by an Illumina MiSeq platform. We developed a filtering approach based on a series of nonarbitrary thresholds established from control samples and from molecular replicates to address the elimination of cross-contamination, PCR/sequencing errors and mistagging artefacts. This resulted in a conservative and informative metabarcoding data set. We developed a taxonomic assignment procedure that combines different approaches and that allowed the identification of ~75% of invertebrate COI variants to the species level. Moreover, based on the diversity of the variants, we introduced a semiquantitative statistic in our diet study, the minimum number of individuals, which is based on the number of distinct variants in each sample. The metabarcoding approach described in this article may guide future diet studies that aim to produce robust data sets associated with a fine and accurate identification of prey items.

Applicability of massively parallel sequencing on monitoring harmful algae at Varna Bay in the Black Sea

In this study the plankton diversity in 13 environmental samples from Varna Bay (in the western Black Sea) was analyzed using massively parallel sequencing (MPS). This preliminary study was undertaken to assess the potential of this technology for future implementation in monitoring programs in the Black Sea. Amplicon sequences of the 18S rRNA gene (V4-5 regions) were obtained using the Illumina MiSeq 250PE platform. A total of 1137 operational taxonomic units (OTUs) were obtained among which 242 OTUs with >0.990 BLAST top hit similarity (21.3% of all detected OTUs) closely related to sequences belonging to -protists. A large portion (175 OTUs=72.3%) was identified at the species levels, including species typical for the Bulgarian Black Sea plankton community, as well as many that haven't been reported earlier in the Bulgarian Black Sea coast (124 OTUs=51.2%). Dinoflagellates were represented by the highest species number (77 OTUs comprising 31.8% of protist species), with dominant genera Gyrodinium and Heterocapsa. The present survey revealed the presence of 12 species listed as harmful, some of which have been previously overlooked, such as Cochlodinium polykrikoides, Karenia bicuneiformis, and Karlodinium veneficum. Species identification was possible for 10.3-36.0% of the detected OTUs in the six major supergroups. The frequency in Rhizaria was significantly lower than that in other major groups (p<0.05-0.01), implying difficulties in the classification from morphology-based observations. The metagenetic data had an insufficient resolution of the 18S rRNA gene for species identification in many genera. These issues may hamper the implementation of MPS-based surveys for plankton monitoring, especially for detecting harmful algal blooms (HAB). The sequencing technology is steadily improving and it is expected that sequence length and quality issues will be resolved in the near future. The ongoing efforts to register taxonomic information and quality controls in the international nucleotide sequence databases (INSDs) will be essential for improving taxonomic identification power.

Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs

Gut microbiota plays fundamental roles in energy harvest, nutrient digestion, and intestinal health, especially in processing indigestible components of polysaccharides in diet. Unraveling the microbial taxa and functional capacity of gut microbiome associated with feed efficiency can provide important knowledge to improve pig feed efficiency in swine industry. In the current research, we studied the association of fecal microbiota with feed efficiency in 280 commercial Duroc pigs. All experimental pigs could be clustered into two enterotype-like groups. Different enterotypes showed the tendency of association with the feed efficiency (P = 0.07). We further identified 31 operational taxonomic units (OTUs) showing the potential associations with porcine feed efficiency. These OTUs were mainly annotated to the bacteria related to the metabolisms of dietary polysaccharides. Although we did not identify the RFI-associated bacterial species at FDR < 0.05 level, metagenomic sequencing analysis did find the distinct function capacities of gut microbiome between the high and low RFI pigs (FDR < 0.05). The KEGG orthologies related to nitrogen metabolism, amino acid metabolism, and transport system, and eight KEGG pathways including glycine, serine, and threonine metabolism were positively associated with porcine feed efficiency. We inferred that gut microbiota might improve porcine feed efficiency through promoting intestinal health by the SCFAs produced by fermenting dietary polysaccharides and improving the utilization of dietary protein. The present results provided important basic knowledge for improving porcine feed efficiency through modulating gut microbiome.

Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing

Modern metagenomic environmental DNA studies are almost completely reliant on next-generation sequencing, making evaluations of these methods critical. We compare two next-generation sequencing techniques – amplicon and shotgun – on water samples across four of Brazil’s major river floodplain systems (Amazon, Araguaia, Paraná, and Pantanal). Less than 50% of phyla identified via amplicon sequencing were recovered from shotgun sequencing, clearly challenging the dogma that mid-depth shotgun recovers more diversity than amplicon-based approaches. Amplicon sequencing also revealed ~27% more families. Overall the amplicon data were more robust across both biodiversity and community ecology analyses at different taxonomic scales. Our work doubles the sampling size in similar environmental studies, and novelly integrates environmental data (e.g., pH, temperature, nutrients) from each site, revealing divergent correlations depending on which data are used. While myriad variants on NGS techniques and bioinformatic pipelines are available, our results point to core differences that have not been highlighted in any studies to date. Given the low number of taxa identified when coupling shotgun data with clade-based taxonomic algorithms, previous studies that quantified biodiversity using such bioinformatic tools should be viewed cautiously or re-analyzed. Nonetheless, shotgun has complementary advantages that should be weighed when designing projects.

Insights into study design and statistical analyses in translational microbiome studies

Research questions in translational microbiome studies are substantially more complex than their counterparts in basic science. Robust study designs with appropriate statistical analysis frameworks are pivotal to the success of these translational studies. This review considers how study designs can account for heterogeneous phenotypes by adopting representative sampling schemes for recruiting the study population and making careful choices about the control population. Advantages and limitations of 16S profiling and whole-genome sequencing, the two primary techniques for measuring the microbiome, are discussed followed by an overview of bioinformatic processing of high-throughput sequencing data from these measurements. Practical insights into the downstream statistical analyses including data processing and integration, variable transformations, and data exploration are provided. The merits of regularization and ensemble modeling for analyzing microbiome data are discussed along with a recommendation for selecting modeling approaches based on data-driven simulations and objective evaluation. The review builds on several recent discussions of study design issues in microbiome research but with a stronger emphasis on the downstream and often-ignored aspects of statistical analyses that are crucial for bridging the gap between basic science and translation.

Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.

Strengths and Biases of High-Throughput Sequencing Data in the Characterization of Freshwater Ciliate Microbiomes

Molecular surveys of eukaryotic microbial communities employing high-throughput sequencing (HTS) techniques are rapidly supplanting traditional morphological approaches due to their larger data output and reduced bench work time. Here, we directly compare morphological and Illumina data obtained from the same samples, in an effort to characterize ciliate faunas from sediments in freshwater environments. We show how in silico processing affects the final outcome of our HTS analysis, providing evidence that quality filtering protocols strongly impact the number of predicted taxa, but not downstream conclusions such as biogeography patterns. We determine the abundance distribution of ciliates, showing that a small fraction of abundant taxa dominates read counts. At the same time, we advance reasons to believe that biases affecting HTS abundances may be significant enough to blur part of the underlying biological picture. We confirmed that the HTS approach detects many more taxa than morphological inspections, and highlight how the difference varies among taxonomic groups. Finally, we hypothesize that the two datasets actually correspond to different conceptions of "diversity," and consequently that neither is entirely superior to the other when investigating environmental protists.

Impact of Different Fecal Processing Methods on Assessments of Bacterial Diversity in the Human Intestine

The intestinal microbiota are integral to understanding the relationships between nutrition and health. Therefore, fecal sampling and processing protocols for metagenomic surveys should be sufficiently robust, accurate, and reliable to identify the microorganisms present. We investigated the use of different fecal preparation methods on the bacterial community structures identified in human stools. Complete stools were collected from six healthy individuals and processed according to the following methods: (i) randomly sampled fresh stool, (ii) fresh stool homogenized in a blender for 2 min, (iii) randomly sampled frozen stool, and (iv) frozen stool homogenized in a blender for 2 min, or (v) homogenized in a pneumatic mixer for either 10, 20, or 30 min. High-throughput DNA sequencing of the 16S rRNA V4 regions of bacterial community DNA extracted from the stools showed that the fecal microbiota remained distinct between individuals, independent of processing method. Moreover, the different stool preparation approaches did not alter intra-individual bacterial diversity. Distinctions were found at the level of individual taxa, however. Stools that were frozen and then homogenized tended to have higher proportions of Faecalibacterium, Streptococcus, and Bifidobacterium and decreased quantities of Oscillospira, Bacteroides, and Parabacteroides compared to stools that were collected in small quantities and not mixed prior to DNA extraction. These findings indicate that certain taxa are at particular risk for under or over sampling due to protocol differences. Importantly, homogenization by any method significantly reduced the intra-individual variation in bacteria detected per stool. Our results confirm the robustness of fecal homogenization for microbial analyses and underscore the value of collecting and mixing large stool sample quantities in human nutrition intervention studies.

Microbiome Changes during Tuberculosis and Antituberculous Therapy

The critical role of commensal microbiota in the human body has been increasingly recognized, and our understanding of its implications in human health and disease has expanded rapidly. The lower respiratory tract contains diverse communities of microbes known as lung microbiota, which are present in healthy individuals and in individuals with respiratory diseases. The dysbiosis of the airway microbiota in pulmonary tuberculosis (TB) may play a role in the pathophysiological processes associated with TB disease. Recent studies of the lung microbiome have pointed out changes in lung microbial communities associated with TB and other lung diseases and have also begun to elucidate the profound effects that antituberculous drug therapy can have on the human lung microbiome composition. In this review, the potential role of the human microbiome in TB pathogenesis and the changes in the human microbiome with Mycobacterium tuberculosis infection and TB therapy are presented and discussed.

Analysis and Interpretation of the Human Microbiome

Microbiome research has experienced an unprecedented level of growth over the last decade. This is largely due to revolutionary developments in, and accessibility to, DNA sequencing technologies that have enabled laboratories with even modest budgets to undertake projects. Study of the human microbiome in particular has seen a surge in interest, and although a lot of time and money has been focused on health and disease, the clinical interpretation of these data and the ability of clinicians to understand these studies in the context of disease are less straightforward. Conditions such as inflammatory bowel disease, asthma, and cancer have seen a huge increase in research focused on the role of microbiome in disease pathogenesis, but the ability of clinicians to appraise and use these data is largely lacking. The purpose of this article is to provide an introduction for clinicians and nonclinicians wishing to learn about and engage in microbiome research. It details the background of microbiome research and discusses the process of generating 16S rRNA sequencing data, the most commonly used method for microbiome analysis. We discuss the interpretation of results in a clinical context, commonly used metrics for analysis and discuss future impact and direction for microbiome research. The meteoric rise of genomic medicine to the brink of routine clinical use should be seen as a blueprint for the microbiome; the ability for physicians to understand and interpret these data is vital to this growth and aiding clinicians (and researchers) to participate in further microbiome research.

Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness

Uncovering the phylogenetic composition of microbial community and the potential functional capacity of microbiome in different gut locations is of great importance to pig production. Here we performed a comparative analysis of gut microbiota and metagenomics among jejunum, ileum and cecum in pigs with distinct fatness. 16S rRNA gene sequencing revealed dramatic differences of microbial composition, diversity and species abundance between small intestine and cecum. Clostridium and SMB53 were enriched in the small intestine, while Prevotella, Treponema, Ruminococcus and Faecalibacterium showed a higher abundance in the cecum. Functional capacity analysis of gut microbiome revealed that the microbiome of small intestine plays important roles in the metabolism of small molecule nutrients, while the microbiome of cecum has the stronger ability to degrade xylan, pectin and cellulose. We identified tens of fatness associated-bacterial species including Escherichia spp. that showed a notable increase of relative abundance in all three gut locations of high fatness pigs. We further suggested that the potential pathogens, inflammation process, and microbial metabolism and nutrient sensing are involved in the high fatness of pigs. These results improve our knowledge about microbiota compositions in different gut locations, and give an insight into the effect of gut microbiota on porcine fatness.