The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies

Nanopore-Enabled Microbiome Analysis: Investigating Environmental and Host-Associated Samples in Rainbow Trout Aquaculture

Microbiome sequencing is at the forefront of health management development, and as such, it is becoming of great interest to monitor the microbiome in the aquaculture industry as well. Oxford Nanopore Technologies (ONT) platforms are gaining popularity to study microbial communities, enabling faster sequencing, extended read length, and therefore, improved taxonomic resolution. Despite this, there is a lack of clear guidelines to perform a metabarcoding study, especially when dealing with samples from non-mammalian species, such as aquaculture-related samples. In this article, we provide general guidelines for sampling, nucleic acid extraction, and ONT-based library preparation for both environmental (water, sediment) and host-associated (gill or skin mucus, skin, gut content, or gut mucosa) microbiome analysis. Our procedures focus specifically on rainbow trout (Oncorhynchus mykiss) reared in experimental facilities. However, these protocols can also be transferred to alternative types of samples, such as environmental DNA (eDNA) monitoring from alternative water sources, or to different fish species. The additional challenge posed by the low biomass and limited bacterial diversity inherent in fish-associated microbiomes is addressed through the implementation of troubleshooting solutions. Furthermore, we describe a bioinformatic pipeline starting from raw reads and leading to taxonomic abundance tables using currently available tools and software. Finally, we provide a set of specific guidelines and considerations related to the strategic planning of a microbiome study within the context of aquaculture. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Environmental sample collection Basic Protocol 2: Host-associated sample collection Alternate Protocol: Host-associated sample collection: Alternative sample types Basic Protocol 3: Sample pre-treatment and nucleic acid extraction Basic Protocol 4: Quality control and preparation for 16S rRNA gene sequencing Support Protocol 1: Assessment of inhibition by quantitative PCR Support Protocol 2: Bioinformatic analysis from raw files to taxonomic abundance tables.

The prevalence of controls in phyllosphere microbiome research: a methodological review

DNA contamination can critically confound microbiome studies. Here, we take a systematic approach to review the current literature and investigate the prevalence of contamination controls in phyllosphere microbiome research over the past decade. By utilising systematic review principles for this review, we were able to conduct a thorough investigation, screening 450 articles from three databases for eligibility and extracting data in a controlled and methodical manner. Worryingly, we observed a surprisingly low usage of both positive and negative contamination controls in phyllosphere research. As a result, we propose a set of minimum standards to combat the effects of contamination in future phyllosphere research.

Microbial perspective of inhibited carbon turnover in Tangel humus of the Northern Limestone Alps

Tangel humus primarily occurs in montane and subalpine zones of the calcareous Alps that exhibit low temperatures and high precipitation sums. This humus form is characterized by inhibited carbon turnover and accumulated organic matter, leading to the typical thick organic layers. However, the reason for this accumulation of organic matter is still unclear, and knowledge about the microbial community within Tangel humus is lacking. Therefore, we investigated the prokaryotic and fungal communities along with the physical and chemical properties within a depth gradient (0-10, 10-20, 20-30, 30-40, 40-50 cm) of a Tangel humus located in the Northern Limestone Alps. We hypothesized that humus properties and microbial activity, biomass, and diversity differ along the depth gradient and that microbial key players refer to certain humus depths. Our results give the first comprehensive information about microbiota within the Tangel humus and establish a microbial zonation of the humus. Microbial activity, biomass, as well as microbial alpha diversity significantly decreased with increasing depths. We identified microbial biomarkers for both, the top and the deepest depth, indicating different, microbial habitats. The microbial characterization together with the established nutrient deficiencies in the deeper depths might explain reduced C-turnover and Tangel humus formation.

Sugarcane mill mud-induced putative host (soybean (Glycine max))-rhizobia symbiosis in sandy loam soil

Domestic production of controlled-release, compost-based, and microbe-enhanced fertilizers is being expanded in the U.S. as a part of rural development. Sugarcane mill mud is a sterilized (≈90°C) agricultural byproduct in surplus that has received interests as a soil amendment in several Southern states, because of its high phosphorus and organic carbon contents. Addition of mill mud to sandy loam significantly increased the nodule formation compared to fertilized and unfertilized controls. Mill mud addition also resulted in pod yields similar to the fertilized control. Though not found in mill mud itself, mill mud additions correlated with an increase in soil Rhizobia as determined by deep 16S rRNA gene sequencing. We hypothesize that Firmicutes in sterilized mill mud induced Rhizobia that in turn enhanced soybean (Glycine max) growth. Collectively, mill mud enhanced the plant growth promoting bacteria when applied to a silt loam, although the relative influence of mill mud-derived bacteria, organic carbon, and nutrients is yet to be determined.

Microbiome depiction through user-adapted bioinformatic pipelines and parameters

Introduction. The role of the microbiome in health and disease continues to be increasingly recognized. However, there is significant variability in the bioinformatic protocols for analysing genomic data. This, in part, has impeded the potential incorporation of microbiomics into the clinical setting and has challenged interstudy reproducibility. In microbial compositional analysis, there is a growing recognition for the need to move away from a one-size-fits-all approach to data processing.Gap Statement. Few evidence-based recommendations exist for setting parameters of programs that infer microbiota community profiles despite these parameters significantly impacting the accuracy of taxonomic inference.Aim. To compare three commonly used programs (DADA2, QIIME2, and mothur) and optimize them into four user-adapted pipelines for processing paired-end amplicon reads. We aim to increase the accuracy of compositional inference and help standardize microbiomic protocol.Methods. Two key parameters were isolated across four pipelines: filtering sequence reads based on a whole-number error threshold (maxEE) and truncating read ends based on a quality score threshold (QTrim). Closeness of sample inference was then evaluated using a mock community of known composition.Results. We observed that raw genomic data lost were proportionate to how stringently parameters were set. Exactly how much data were lost varied by pipeline. Accuracy of sample inference correlated with increased sequence read retention. Falsely detected taxa and unaccounted for microbial constituents were unique to pipeline and parameter. Implementation of optimized parameter values led to better approximation of the known mock community.Conclusions. Microbial compositions generated based on the 16S rRNA marker gene should be interpreted with caution. To improve microbial community profiling, bioinformatic protocols must be user-adapted. Analysis should be performed with consideration for the select target amplicon, pipelines and parameters used, and taxa of interest.

Infection density pattern of Cardinium affects the responses of bacterial communities in an invasive whitefly under heat conditions

Communities of bacteria, especially symbionts, are vital for the growth and development of insects and other arthropods, including Bemisia tabaci Mediterranean (MED), a destructive and invasive insect pest. However, the infection density patterns and influence factors of bacteria in whiteflies, which mainly include symbionts, remain largely unclear. To reveal the different density patterns of Cardinium in B. tabaci MED populations and the impacts of high temperatures on whiteflies with different Cardinium density infection patterns, 2 isofemale lines isolated from B. tabaci MED from the same geographical population of China and from B. tabaci MED collected from other countries and locations were examined using several techniques and methods, including fluorescence in situ hybridization (FISH), quantitative real-time polymerase chain reaction (qPCR), 16S rRNA gene sequencing, and 2b-RAD sequencing. The results showed that there were 2 different infection density patterns of Cardinium in B. tabaci MED (including 1 high-density pattern and 1 low-density pattern). For whiteflies with low-density Cardinium, conventional PCR could not detect Cardinium, but the other techniques confirmed that there was a low level of Cardinium within hosts. High temperature significantly decreased the diversity of bacterial communities: the relative titer of Cardinium increased but the density of Rickettsia decreased in the isofemale line with high-density Cardinium. However, high temperature did not influence the diversity and symbiont density in the line with low-density Cardinium. Moreover, high temperature influenced the functions of bacterial communities in whiteflies with high-density Cardinium but did not affect the bacterial functions in whiteflies with low-density Cardinium. Our results provide novel insights into the complex associations between symbionts and host insects.

Three marine species of the genus Fulvivirga, rich sources of carbohydrate-active enzymes degrading alginate, chitin, laminarin, starch, and xylan

Bacteroidota is a group of marine polysaccharide degraders, which play a crucial role in the carbon cycle in the marine ecosystems. In this study, three novel gliding strains, designated as SS9-22^T, W9P-11^T, and SW1-E11^T, isolated from algae and decaying wood were proposed to represent three novel species of the genus Fulvivirga. We identified a large number of genes encoding for carbohydrate-active enzymes, which potentially participate in polysaccharide degradation, based on whole genome sequencing. The 16S rRNA sequence similarities among them were 94.4-97.2%, and against existing species in the genus Fulvivirga 93.1-99.8%. The complete genomes of strains SS9-22^T, W9P-11^T, and SW1-E11^T comprised one circular chromosome with size of 6.98, 6.52, and 6.39 Mb, respectively; the GC contents were 41.9%, 39.0%, and 38.1%, respectively. The average nucleotide identity and the digital DNA-DNA hybridization values with members in the genus Fulvivirga including the isolates were in a range of 68.9-85.4% and 17.1-29.7%, respectively, which are low for the proposal of novel species. Genomic mining in three genomes identified hundreds of carbohydrate-active enzymes (CAZymes) covering up to 93 CAZyme families and 58-70 CAZyme gene clusters, exceeding the numbers of genes present in the other species of the genus Fulvivirga. Polysaccharides of alginate, chitin, laminarin, starch, and xylan were degraded in vitro, highlighting that the three strains are rich sources of CAZymes of polysaccharide degraders for biotechnological applications. The phenotypic, biochemical, chemotaxonomic, and genomic characteristics supported the proposal of three novel species in the genus Fulvivirga, for which the names Fulvivirga ulvae sp. nov. (SS9-22^T = KCTC 82072^T = GDMCC 1.2804^T), Fulvivirga ligni sp. nov. (W9P-11^T = KCTC 72992^T = GDMCC 1.2803^T), and Fulvivirga maritima sp. nov. (SW1-E11^T = KCTC 72832^T = GDMCC 1.2802^T) are proposed.

Glyphosate-based herbicide use affects individual microbial taxa in strawberry endosphere but not the microbial community composition

AIMS

In a field study, the effects of treatments of glyphosate-based herbicides (GBHs) in soil, alone and in combination with phosphate fertilizer, were examined on the performance and endophytic microbiota of garden strawberry.

METHODS AND RESULTS

The root and leaf endophytic microbiota of garden strawberries grown in GBH-treated and untreated soil, with and without phosphate fertilizer, were analyzed. Next, bioinformatics analysis on the type of 5-enolpyruvylshikimate-3-phosphate synthase enzyme was conducted to assess the potential sensitivity of strawberry-associated bacteria and fungi to glyphosate, and to compare the results with field observations. GBH treatments altered the abundance and/or frequency of several operational taxonomic units (OTUs), especially those of root-associated fungi and bacteria. These changes were partly related to their sensitivity to glyphosate. Still, GBH treatments did not shape the overall community structure of strawberry microbiota or affect plant performance. Phosphate fertilizer increased the abundance of both glyphosate-resistant and glyphosate-sensitive bacterial OTUs, regardless of the GBH treatments.

CONCLUSIONS

These findings demonstrate that although the overall community structure of strawberry endophytic microbes is not affected by GBH use, some individual taxa are.

Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems

BACKGROUND

Microbial communities in recirculating aquaculture systems (RAS) play a role in system success, nutrient cycling, and water quality. Considering the increasing socio-economic role of fish farming, e.g., regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective, especially regarding the growth, development, and welfare of the farmed animal. However, the current data on the composition of microbial communities within RAS is patchy, which is partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems.

RESULTS

We compared sequencing approach performances (3 types of 16S short amplicon sequencing, PacBio long-read amplicon sequencing, and amplification-free shotgun metagenomics) in the characterization of microbial communities in two commercial RAS fish farms. Results showed that 16S primer choice and amplicon length affect some values (e.g., diversity measures, number of assigned taxa or distinguishing ASVs) but have no impact on spatio-temporal patterns between sample types, farms and time points. This implies that 16S rRNA approaches are adequate for community studies. The long-read amplicons underperformed regarding the quantitative resolution of spatio-temporal patterns but were suited to identify functional services, e.g., nitrification cycling and the detection of pathogens. Finally, shotgun metagenomics extended the picture to fungi, viruses, and bacteriophages, opening avenues for exploring inter-domain interactions. All sequencing datasets agreed on major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, and Proteobacteria.

CONCLUSION

The different sequencing approaches yielded overlapping and highly complementary results, with each contributing unique data not obtainable with the other approaches. We conclude that a tiered approach constitutes a strategy for obtaining the maximum amount of information on aquaculture microbial communities and can inform basic research on community evolution dynamics. For specific and/or applied questions, single-method approaches are more practical and cost-effective and could lead to better farm management practices.

Characterization of Bacillus subtilis bacteriophage BasuTN3 isolated from Thua Nao, a thai fermented soybean food product

The infection of bacteriophage is of great concern in food industry as this can result in complete fermentation failure. In this study, a virulent bacteriophage, named BasuTN3, was isolated from Thua Nao, a Thai fermented soybean. The stability of BasuTN3 was evaluated under various ranges of temperature, pH, chloroform, UV, and disinfectants. The results showed that the isolated BasuTN3 appeared to be specific to its bacterial host, which was identified as Bacillus subtilis strain TN3 based on the 16 S rRNA gene sequence analysis. Under TEM, the BasuTN3 belonged to the family Myoviridae. The isolated BasuTN3 could withstand wide temperature ranges (4-45 °C) and pH conditions (5-11). The BasuTN3 was susceptible to chloroform, UV, and commonly used disinfectants. The results obtained expand the knowledge of the Bacillus bacteriophage diversity in the fermented soybean products and provide useful information for the bacteriophage and its bacterial starter cultures.

Epichloë Endophytes Shape the Foliar Endophytic Fungal Microbiome and Alter the Auxin and Salicylic Acid Phytohormone Levels in Two Meadow Fescue Cultivars

Plants harbor a large diversity of endophytic microbes. Meadow fescue (Festuca pratensis) is a cool-season grass known for its symbiotic relationship with the systemic and vertically-via seeds-transmitted fungal endophyte Epichloë uncinata, yet its effects on plant hormones and the microbial community is largely unexplored. Here, we sequenced the endophytic bacterial and fungal communities in the leaves and roots, analyzing phytohormone concentrations and plant performance parameters in Epichloë-symbiotic (E+) and Epichloë-free (E-) individuals of two meadow fescue cultivars. The endophytic microbial community differed between leaf and root tissues independent of Epichloë symbiosis, while the fungal community was different in the leaves of Epichloë-symbiotic and Epichloë-free plants in both cultivars. At the same time, Epichloë symbiosis decreased salicylic acid and increased auxin concentrations in leaves. Epichloë-symbiotic plants showed higher biomass and higher seed mass at the end of the season. Our results demonstrate that Epichloë symbiosis alters the leaf fungal microbiota, which coincides with changes in phytohormone concentrations, indicating that Epichloë endophytes affect both plant immune responses and other fungal endophytes. Whether the effect of Epichloë endophytes on other fungal endophytes is connected to changes in phytohormone concentrations remains to be elucidated.

Honeybees affect floral microbiome composition in a central food source for wild pollinators in boreal ecosystems

Basic knowledge on dispersal of microbes in pollinator networks is essential for plant, insect, and microbial ecology. Thorough understanding of the ecological consequences of honeybee farming on these complex plant-pollinator-microbe interactions is a prerequisite for sustainable honeybee keeping. Most research on plant-pollinator-microbe interactions have focused on temperate agricultural systems. Therefore, information on a wild plant that is a seasonal bottleneck for pollinators in cold climate such as Salix phylicifolia is of specific importance. We investigated how floral visitation by insects influences the community structure of bacteria and fungi in Salix phylicifolia inflorescences under natural conditions. Insect visitors were experimentally excluded with net bags. We analyzed the microbiome and measured pollen removal in open and bagged inflorescences in sites where honeybees were foraging and in sites without honeybees. Site and plant individual explained most of the variation in floral microbial communities. Insect visitation and honeybees had a smaller but significant effect on the community composition of microbes. Honeybees had a specific effect on the inflorescence microbiome and, e.g., increased the relative abundance of operational taxonomic units (OTUs) from the bacterial order Lactobacillales. Site had a significant effect on the amount of pollen removed from inflorescences but this was not due to honeybees. Insect visitors increased bacterial and especially fungal OTU richness in the inflorescences. Pollinator visits explained 38% variation in fungal richness, but only 10% in bacterial richness. Our work shows that honeybee farming affects the floral microbiome in a wild plant in rural boreal ecosystems.

Alterations in fecal β-defensin-3 secretion as a marker of instability of the gut microbiota

Compositional changes in the microbiota (dysbiosis) may be a basis for Irritable Bowel Syndrome (IBS), but biomarkers are currently unavailable to direct microbiota-directed therapy. We therefore examined whether changes in fecal β-defensin could be a marker of dysbiosis in a murine model. Experimental dysbiosis was induced using four interventions relevant to IBS: a mix of antimicrobials, westernized diets (high-fat/high-sugar and high salt diets), or mild restraint stress. Fecal mouse β-defensin-3 and 16S rRNA-based microbiome profiles were assessed at baseline and during and following these interventions. Each intervention, except for mild restraint stress, altered compositional and diversity profiles of the microbiota. Exposure to antimicrobials or a high-fat/high-sugar diet, but not mild restraint stress, resulted in decreased fecal β-defensin-3 compared to baseline. In contrast, exposure to the high salt diet increased β-defensin-3 compared to baseline. Mice exposed to the mix of antimicrobials showed the largest compositional changes and the most significant correlations between β-defensin-3 levels and bacterial diversity. The high salt diet was also associated with significant correlations between changes in β-defensin-3 and bacterial diversity, and this was not accompanied by discernible inflammatory changes in the host. Thus, dietary change or antimicrobial exposure, both recognized factors in IBS exacerbations, induced marked dysbiosis that was accompanied by changes in fecal β-defensin-3 levels. We propose that serial monitoring of fecal β-defensins may serve as a marker of dysbiosis and help identify those IBS patients who may benefit from microbiota-directed therapeutic interventions.

Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain)

Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.

Chemical and microbial characterization of sugarcane mill mud for soil applications

Sugarcane mill mud/filter cake is an activated sludge-like byproduct from the clarifier of a raw sugar production factory, where cane juice is heated to ≈90°C for 1–2 hr, after the removal of bagasse. Mill mud is enriched with organic carbon, nitrogen, and nutrient minerals; no prior report utilized 16S rRNA gene sequencing to characterize the microbial composition. Mill mud could be applied to agricultural fields as biofertilizer to replace or supplement chemical fertilizers, and as bio-stimulant to replenish microorganisms and organic carbon depleted by erosion and post-harvest field burning. However, mill mud has historically caused waste management challenges in the United States. This study reports on the chemical and microbial (16S rRNA) characteristics for mill muds of diverse origin and ages. Chemical signature (high phosphorus) distinguished mill mud from bagasse (high carbon to nitrogen (C/N) ratio) and soil (high pH) samples of diverse geographical/environmental origins. Bacterial alpha diversity of all sample types (mill mud, bagasse, and soil) was inversely correlated with C/N. Firmicutes dominated the microbial composition of fresh byproducts (mill mud and bagasse) as-produced within the operating factory. Upon aging and environmental exposure, the microbial community of the byproducts diversified to resemble that of soils, and became dominated by varying proportions of other phyla such as Acidobacteria, Chloroflexi, and Planctomyces. In summary, chemical properties allowed grouping of sample types (mill mud, bagasse, and soil-like), and microbial diversity analyses visualized aging caused by outdoor exposures including soil amendment and composting. Results suggest that a transient turnover of microbiome by amendments shifts towards more resilient population governed by the chemistry of bulk soil.

Soil microbial communities shift along an urban gradient in Berlin, Germany

The microbial communities inhabiting urban soils determine the functioning of these soils, in regards to their ability to cycle nutrients and support plant communities. In an increasingly urbanized world these properties are of the utmost importance, and the microbial communities responsible are worthy of exploration. We used 53 grassland sites spread across Berlin to describe and explain the impacts of urbanity and other environmental parameters upon the diversity and community composition of four microbial groups. These groups were (i) the Fungi, with a separate dataset for (ii) the Glomeromycota, (iii) the Bacteria, and (iv) the protist phylum Cercozoa. We found that urbanity had distinct impacts on fungal richness, which tended to increase. Geographic distance between sites and soil chemistry, in addition to urbanity, drove microbial community composition, with site connectivity being important for Glomeromycotan communities, potentially due to plant host communities. Our findings suggest that many microbial species are well adapted to urban soils, as supported by an increase in diversity being a far more common result of urbanity than the reverse. However, we also found distinctly separate distributions of operational taxonomic unit (OTU)s from the same species, shedding doubt of the reliability of indicator species, and the use of taxonomy to draw conclusion on functionality. Our observational study employed an extensive set of sites across an urbanity gradient, in the region of the German capital, to produce a rich microbial dataset; as such it can serve as a blueprint for other such investigations.

The comparison of changes in fecal and mucosal microbiome in metabolic endotoxemia induced by a high-fat diet

The aim of this study was to compare the mucosal and fecal microbiota in a high fat diet-induced metabolic endotoxemia (ME) model and to identify potential species that represent dysbiosis and might mediate the inflammatory process. Fourteen male wistar albino rats were fed a standard diet (n = 7) and a high-fat diet (HFD) (n = 7). The standard diet (2600 kcal/kg) contained 3% of energy from fat and HFD (6740 kcal/kg) contained 67% beef tallow. After feeding for 12 weeks, all rats were sacrificed after fasting for 12 h and blood samples were collected. Fresh faecal samples and descending colon samples of rats were collected in sterile plastic tubes using a clean technique, immediately snap-frozen in liquid nitrogen, and then stored at -80 °C until used for analysis. Serum glucose, TRG, TLR4, LPS, and fecal LPS increased in the HFD group. On the contrary, HDL was higher and statistically significant in the CD group. The levels of IL-6 and TNF-α in the colon tissue of the HFD group were significant. The HFD group caused a significant increase in LPS levels in serum and feces. In addition, the gut and mucosal microbiome were positively/negatively correlated with the ME markers (IL6, TNFα, LPS). The results showed that gut and mucosal microbiome changes were associated with HFD. These changes were dense at species levels. The current study demonstrated changes in gut and mucosal microbiota in HFD-induced metabolic endotoxemia.

Optimization and Evaluation of the 30S-S11 rRNA Gene for Taxonomic Profiling of Oral Streptococci

Dental caries is a multifactorial disease driven by interactions between the highly complex microbial biofilm community and host factors like diet, oral hygiene habits, and age. The oral streptococci are one of the most dominant members of the plaque biofilm and are implicated in disease but also in maintaining oral health. Current methods used for studying the supragingival plaque community commonly sequence portions of the16S rRNA gene, which often cannot taxonomically resolve members of the streptococcal community past the genus level due to their sequence similarity. The goal of this study was to design and evaluate a more reliable and cost-effective method to identify oral streptococci at the species level by applying a new locus, the 30S-S11 rRNA gene, for high-throughput amplicon sequencing. The study results demonstrate that the newly developed single-copy 30S-S11 gene locus resolved multiple amplicon sequence variants (ASVs) within numerous species, providing much improved taxonomic resolution over 16S rRNA V4. Moreover, the results reveal that different ASVs within a species were found to change in abundance at different stages of caries progression. These findings suggest that strains of a single species may perform distinct roles along a biochemical spectrum associated with health and disease. The improved identification of oral streptococcal species will provide a better understanding of the different ecological roles of oral streptococci and inform the design of novel oral probiotic formulations for prevention and treatment of dental caries. IMPORTANCE The microbiota associated with the initiation and progression of dental caries has yet to be fully characterized. Although much insight has been gained from 16S rRNA hypervariable region DNA sequencing, this approach has several limitations, including poor taxonomic resolution at the species level. This is particularly relevant for oral streptococci, which are abundant members of oral biofilm communities and major players in health and caries disease. Here, we develop a new method for taxonomic profiling of oral streptococci based on the 30S-S11 rRNA gene, which provides much improved resolution over 16S rRNA V4 (resolving 10 as opposed to 2 species). Importantly, 30S-S11 can resolve multiple amplicon sequence variants (ASVs) within species, providing an unprecedented insight into the ecological progression of caries. For example, our findings reveal multiple incidences of different ASVs within a species with contrasting associations with health or disease, a finding that has high relevance toward the informed design of prebiotic and probiotic therapy.

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

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

Horsenettle (Solanum carolinense) fruit bacterial communities are not variable across fine spatial scales

Fruit house microbial communities that are unique from the rest of the plant. While symbiotic microbial communities complete important functions for their hosts, the fruit microbiome is often understudied compared to other plant organs. Fruits are reproductive tissues that house, protect, and facilitate the dispersal of seeds, and thus they are directly tied to plant fitness. Fruit microbial communities may, therefore, also impact plant fitness. In this study, we assessed how bacterial communities associated with fruit of Solanum carolinense, a native herbaceous perennial weed, vary at fine spatial scales (<0.5 km). A majority of the studies conducted on plant microbial communities have been done at large spatial scales and have observed microbial community variation across these large spatial scales. However, both the environment and pollinators play a role in shaping plant microbial communities and likely have impacts on the plant microbiome at fine scales. We collected fruit samples from eight sampling locations, ranging from 2 to 450 m apart, and assessed the fruit bacterial communities using 16S rRNA gene amplicon sequencing. Overall, we found no differences in observed richness or microbial community composition among sampling locations. Bacterial community structure of fruits collected near one another were not more different than those that were farther apart at the scales we examined. These fine spatial scales are important to obligate out-crossing plant species such as S. carolinense because they are ecologically relevant to pollinators. Thus, our results could imply that pollinators serve to homogenize fruit bacterial communities across these smaller scales.

Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities

Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.

Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels

The quantification of the total microbial content in metagenomic samples is critical for investigating the interplay between the microbiome and its host, as well as for assessing the accuracy and precision of the relative microbial composition which can be strongly biased in low microbial biomass samples. In the present study, we demonstrate that digital droplet PCR (ddPCR) can provide accurate quantification of the total copy number of the 16S rRNA gene, the gene usually exploited for assessing total bacterial abundance in metagenomic DNA samples. Notably, using DNA templates with different integrity levels, as measured by the DNA integrity number (DIN), we demonstrated that 16S rRNA copy number quantification is strongly affected by DNA quality and determined a precise correlation between quantification underestimation and DNA degradation levels. Therefore, we propose an input DNA mass correction, according to the observed DIN value, which could prevent inaccurate quantification of 16S copy number in degraded metagenomic DNAs. Our results highlight that a preliminary evaluation of the metagenomic DNA integrity should be considered before performing metagenomic analyses of different samples, both for the assessment of the reliability of observed differential abundances in different conditions and to obtain significant functional insights.

Designing specific bacterial 16S primers to sequence and quantitate plant endo-bacteriome

Plant endophytic bacteria colonize the internal tissues of plants and interact with plants closely. The past two decades have witnessed the increasing application of next-generation 16S rRNA gene sequencing in the investigation of bacterial communities. However, deciphering plant endo-bacterial communities by this method is difficult because of the co-amplification of massive plant organellar DNAs with bacterial 16S. Here, we designed polymerase chain reaction (PCR) primer sets, including 799F/1107R, 322F/796R, and 322F-Dr/796Rs (primer pair 322F/796R with a penultimate-base substitution in 322F), that can specifically amplify bacterial 16S from plant total DNAs. We computationally and experimentally evaluated the specificity, coverage, and accuracy of the newly designed primer sets. Both 799F/1107R and 322F-Dr/796Rs produced plant DNA-free 16S amplicon libraries or reduced plant DNA contamination to lower than 5% for the plant materials with extremely-low-abundance bacterial communities. The primer set 322F-A/796R was used through absolute quantitative PCR to quantitate the population size of rice leaf or root endo-bacteriome, which revealed 10⁶-10⁷ and 10⁹-10¹⁰ bacteria per gram fresh weight, respectively. These 16S primer sets and amplification methods enable the simple and inexpensive next-generation sequencing and quantification of plant endo-bacteriome, which will significantly advance studies on the plant-related microbiome.

The growth of plants and indigenous bacterial community were significantly affected by cadmium contamination in soil-plant system

Concentrations of heavy metals continue to increase in soil environments as a result of both anthropogenic activities and natural processes. Cadmium (Cd) is one of the most toxic heavy metals and poses health risks to both humans and the ecosystem. Herein, we explore the impacts of Cd on a soil-plant system composed of oilseed rapes (Brassica napus and Brassica juncea) and bacteria. The results showed that Cd accumulation within tissues of two species of oilseed rapes enhanced with increasing concentrations of Cd in soils, and Cd treatment decreased their chlorophyll content and suppressed rapeseeds growth. Meanwhile, Cd stress induced the changes of antioxidative enzymes activities of both B. napus and B. juncea. Response to Cd of bacterial community was similar in soil-two species of oilseed rapes system. The impact of Cd on the bacterial communities of soils was greater than bacterial communities of plants (phyllosphere and endophyte). The α-diversity of bacterial community in soils declined significantly under higher Cd concentration (30 mg/kg). In addition, soil bacterial communities composition and structure were altered in the presence of higher Cd concentration. Meanwhile, the bacterial communities of bulk soils were significantly correlated with Cd, while the variation of rhizosphere soils bacterial communities were markedly correlated with Cd and other environmental factors of both soils and plants. These results suggested that Cd could affect both the growth of plants and the indigenous bacterial community in soil-plant system, which might further change ecosystem functions in soils.

Low microbial biomass within the reproductive tract of mid-lactation dairy cows: A study approach

The microbiome from the reproductive tract is being investigated for its putative effect on fertility, embryo development, and health status of the human or animal host postpartum. Besides the presence of a vaginal microbiome, recent studies have claimed the existence and putative role of the uterine microbiome. Yet, the extremely low bacterial numbers and high eukaryotic/prokaryotic DNA ratio make this a highly challenging environment to study with next-generation sequencing (NGS) techniques. Here, we describe the methodological challenges that are typically encountered when performing an accurate analysis of low microbial biomass samples, illustrated by data of our own observational study. In terms of the research question, we compared the microbial composition throughout different parts of the reproductive tract of clinically healthy, mid-lactation Holstein-Friesian cows. Samples were collected from 5 dairy cows immediately after killing. Swabs were taken from the vagina, and from 4 pre-established locations of the uterine endometrium. In addition to the conventional DNA extraction blank controls, sterile swabs rubbed over disinfected disposable gloves and the disinfected surface of the uterus (tunica serosa) before incision were taken as sampling controls. The DNA extraction, DNA quantification, quantitative PCR of the 16S rRNA genes, and 16S rRNA gene sequencing were performed. In terms of NGS data analysis, we performed prevalence-based filtering of putative contaminant operational taxonomic units (OTU) using the decontam R package. Although the bacterial composition differed between the vagina and uterus, no differences in bacterial community structure (α and β diversity) were found among the different locations in the uterus. At phylum level, uterine samples had a greater relative abundance of Proteobacteria, and a lesser relative abundance of Firmicutes than vaginal samples. The number of shared OTU between vagina and uterus was limited, suggesting the existence of bacterial transmission routes other than the transcervical one to the uterus. The mid-lactation bovine genital tract is a low microbial biomass environment, which makes it difficult to distinguish between its constitutive versus contaminant microbiome. The integration of key controls is therefore strictly necessary to decrease the effect of accidentally introduced contaminant sequences and improve the reliability of results in samples with low microbial biomass.

The Gut Microbiome in Schizophrenia and the Potential Benefits of Prebiotic and Probiotic Treatment

The gut microbiome (GMB) plays an important role in developmental processes and has been implicated in the etiology of psychiatric disorders. However, the relationship between GMB and schizophrenia remains unclear. In this article, we review the existing evidence surrounding the gut microbiome in schizophrenia and the potential for antipsychotics to cause adverse metabolic events by altering the gut microbiome. We also evaluate the current evidence for the clinical use of probiotic and prebiotic treatment in schizophrenia. The current data on microbiome alteration in schizophrenia remain conflicting. Longitudinal and larger studies will help elucidate the confounding effect on the microbiome. Current studies help lay the groundwork for further investigations into the role of the GMB in the development, presentation, progression and potential treatment of schizophrenia.

Diversity and Physiological Characteristics of Antarctic Lichens-Associated Bacteria

The diversity of lichen-associated bacteria from lichen taxa Cetraria, Cladonia, Megaspora, Pseudephebe, Psoroma, and Sphaerophorus was investigated by sequencing of 16S rRNA gene amplicons. Physiological characteristics of the cultured bacterial isolates were investigated to understand possible roles in the lichen ecosystem. Proteobacteria (with a relative abundance of 69.7–96.7%) were mostly represented by the order Rhodospirillales. The 117 retrieved isolates were grouped into 35 phylotypes of the phyla Actinobacteria (27), Bacteroidetes (6), Deinococcus-Thermus (1), and Proteobacteria (Alphaproteobacteria (53), Betaproteobacteria (18), and Gammaproteobacteria (12)). Hydrolysis of macromolecules such as skim milk, polymer, and (hypo)xanthine, solubilization of inorganic phosphate, production of phytohormone indole-3-acetic acid, and fixation of atmospheric nitrogen were observed in different taxa. The potential phototrophy of the strains of the genus Polymorphobacter which were cultivated from a lichen for the first time was revealed by the presence of genes involved in photosynthesis. Altogether, the physiological characteristics of diverse bacterial taxa from Antarctic lichens are considered to imply significant roles of lichen-associated bacteria to allow lichens to be tolerant or competitive in the harsh Antarctic environment.

Evaluation of Established Methods for DNA Extraction and Primer Pairs Targeting 16S rRNA Gene for Bacterial Microbiota Profiling of Olive Xylem Sap

Next-generation sequencing has revolutionized our ability to investigate the microbiota composition of diverse and complex environments. However, a number of factors can affect the accuracy of microbial community assessment, such as the DNA extraction method, the hypervariable region of 16S rRNA gene targeted, or the PCR primers used for amplification. The aim of this study was to assess the influence of commercially available DNA extraction kits and different primer pairs to provide a non-biased vision of the composition of bacterial communities present in olive xylem sap. For that purpose, branches from "Picual" and "Arbequina" olive cultivars were used for xylem sap extraction using a Scholander chamber device. The DNA extraction protocol significantly affected xylem sap bacterial community assessment. That resulted in significant differences in alpha (Richness) and beta diversity (UniFrac distances) metrics among DNA extraction protocols, with the 12 DNA extraction kits evaluated being clustered in four groups behaving differently. Although the core number of taxa detected by all DNA extraction kits included four phyla, seven classes, 12 orders, 16 or 21 families, and 12 or 14 genera when using the Greengenes or Silva database for taxonomic assignment, respectively, some taxa, particularly those identified at low frequency, were detected by some DNA extraction kits only. The most accurate depiction of a bacterial mock community artificially inoculated on sap samples was generated when using the PowerPlant DNA extraction kit, the combination of 799F/1193R primers amplifying the hypervariable V5-V7 region, and the Silva 132 database for taxonomic assignment. The DESeq2 analysis displayed significant differences among genera abundance between the different PCR primer pairs tested. Thus, Enterobacter, Granulicatella, Prevotella, and Brevibacterium presented a significant higher abundance in all PCR protocols when compared with primer pair 799F/1193R, while the opposite was true for Pseudomonas and Pectobacterium. The methodological approach followed in this study can be useful to optimize plant-associated microbiome analysis, especially when exploring new plant niches. Some of the DNA extraction kits and PCR primers selected in this study will contribute to better characterize bacterial communities inhabiting the xylem sap of olives or other woody crop species.

Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing

Short-amplicon 16S rRNA gene sequencing is currently the method of choice for studies investigating microbiomes. However, comparative studies on differences in procedures are scarce. We sequenced human stool samples and mock communities with increasing complexity using a variety of commonly used protocols. Short amplicons targeting different variable regions (V-regions) or ranges thereof (V1-V2, V1-V3, V3-V4, V4, V4-V5, V6-V8, and V7-V9) were investigated for differences in the composition outcome due to primer choices. Next, the influence of clustering (operational taxonomic units [OTUs], zero-radius OTUs [zOTUs], and amplicon sequence variants [ASVs]), different databases (GreenGenes, the Ribosomal Database Project, Silva, the genomic-based 16S rRNA Database, and The All-Species Living Tree), and bioinformatic settings on taxonomic assignment were also investigated. We present a systematic comparison across all typically used V-regions using well-established primers. While it is known that the primer choice has a significant influence on the resulting microbial composition, we show that microbial profiles generated using different primer pairs need independent validation of performance. Further, comparing data sets across V-regions using different databases might be misleading due to differences in nomenclature (e.g., Enterorhabdus versus Adlercreutzia) and varying precisions in classification down to genus level. Overall, specific but important taxa are not picked up by certain primer pairs (e.g., Bacteroidetes is missed using primers 515F-944R) or due to the database used (e.g., Acetatifactor in GreenGenes and the genomic-based 16S rRNA Database). We found that appropriate truncation of amplicons is essential and different truncated-length combinations should be tested for each study. Finally, specific mock communities of sufficient and adequate complexity are highly recommended.

IMPORTANCE In 16S rRNA gene sequencing, certain bacterial genera were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings. Concerning the last, quality thresholds as well as bioinformatic settings (i.e., clustering approach, analysis pipeline, and specific adjustments such as truncation) are responsible for a number of observed differences between studies. Conclusions drawn by comparing one data set to another (e.g., between publications) appear to be problematic and require independent cross-validation using matching V-regions and uniform data processing. Therefore, we highlight the importance of a thought-out study design including sufficiently complex mock standards and appropriate V-region choice for the sample of interest. The use of processing pipelines and parameters must be tested beforehand.

DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions

Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.

Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau

High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3-V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.

Sorption-desorption and biodegradation of sulfometuron-methyl and its effects on the bacterial communities in Amazonian soils amended with aged biochar

Sulfometuron-methyl is a broad-spectrum herbicide, used throughout Brazil; however, its environmental impacts in biochar (BC) amended soils is not fully understood. Biochar is known to enhance soil quality but can also have undesired effects such as altering the bioavailability and behavior of herbicides. Microbial communities can degrade herbicides such as sulfometuron-methyl in soils; however, they are known to be affected by BC. Therefore, it is important to understand the tripartite interaction between these factors. This research aimed to evaluate the sorption-desorption and biodegradation of sulfometuron-methyl in Amazonian soils amended with BC, and to assess the effects of the interactions between BC and sulfometuron-methyl on soil bacterial communities. Soil samples were collected from field plots amended with BC at three doses (0, 40 and 80 t ha^-1) applied ten years ago. The herbicide sorption and desorption were evaluated using a batch equilibrium method. Mineralization and biodegradation studies were conducted in microcosms incubated with ¹⁴C-sulfometuron-methyl for 80 days. Systematic soil sampling, followed by DNA extraction, quantification (qPCR) and 16S rRNA amplicon sequencing were performed. The presence of BC increased the sorption of the herbicide to the soil by 11% (BC40) and 16% (BC80) compared to unamended soil. The presence of BC also affected the degradation of ¹⁴C-sulfometuron-methyl, reducing the mineralization rate and increasing the degradation half-life times (DT50) from 36.67 days in unamended soil to 52.11 and 55.45 days in BC40 and BC80 soils, respectively. The herbicide application altered the bacterial communities, affecting abundance and richness, and changing the taxonomic diversity (i.e., some taxa were promoted and other inhibited). A tripartite interaction was found between BC, the herbicide and soil bacterial communities, suggesting that it is important to consider the environmental impact of soil applied herbicides in biochar amended soils.

Multicenter assessment of microbial community profiling using 16S rRNA gene sequencing and shotgun metagenomic sequencing

INTRODUCTION

Microbiome research based on high-throughput sequencing has grown exponentially in recent years, but methodological variations can easily undermine the reproducibility across studies.

OBJECTIVES

To systematically evaluate the comparability of sequencing results of 16S rRNA gene sequencing (16Ss)- and shotgun metagenomic sequencing (SMs)-based microbial community profiling in laboratories under routine conditions.

METHODS

We designed a multicenter study across 35 participating laboratories in China using designed mock communities and homogenized fecal samples.

RESULTS

A wide range of practices and approaches was reported by the participating laboratories. The observed microbial compositions of the mock communities in 46.2% (12/26) of the 16Ss and 82.6% (19/23) of the SMs laboratories had significant correlations with the expected result (Spearman r>0.59, P <0.05). The results from laboratories with near-identical protocols showed slight interlaboratory deviations. However, a high degree of interlaboratory deviation was found in the observed abundances of specific taxa, such as Bacteroides spp. (range: 0.3%-53.5%), Enterococci spp. (range: 0.8%-43.9%) and Fusobacterium spp. (range: 0.1%-39.8%). SMs performed better than 16Ss in detecting low-abundance bacteria (B. bifidum). The differences in DNA extraction methods, amplified regions and bioinformatics analysis tools (taxonomic classifiers and database) were important factors causing interlaboratory deviations. Addressing laboratory contamination is an urgent task because various sources of unexpected microbes were found in negative control samples.

CONCLUSIONS

Well-defined control samples, such as the mock communities in this study, should be routinely used in microbiome research for monitoring potential biases. The findings in this study will provide guidance in the choice of more reasonable operating procedures to minimize potential methodological biases in revealing human microbiota composition.

Microbiological Profile and Human Immune Response Associated with Peri-Implantitis: A Systematic Review

PURPOSE

To evaluate and synthesize the existing evidence on the microbiological and human immune response associated with peri-implantitis in comparison to healthy implants.

MATERIALS AND METHODS

Three electronic databases (MEDLINE, Embase, and Cochrane Library) were searched in October 2019 to identify clinical studies evaluating the microbiota and the immune response associated with peri-implantitis. Two reviewers independently screened the studies and used the full text to extract the data. A qualitative synthesis was performed on the extracted data and summary tables were prepared. Due to clinical and methodological heterogeneity among included studies, no meta-analysis was performed.

RESULTS

Forty studies were included in this review. Of these, 20 studies compared the microbiological profile of peri-implantitis with healthy implants. Nineteen studies focused on the immune response associated with peri-implantitis in comparison to healthy implants. Three studies focus on gene polymorphism associated with peri-implantitis. The most commonly reported bacteria associated with peri-implantitis were obligate anaerobe Gram-negative bacteria (OAGNB), asaccharolytic anaerobic Gram-positive rods (AAGPRs), and other Gram-positive species. In regard to immune response, the most frequently reported pro-inflammatory mediators associated with peri-implantitis were IL-1β, IL-6, IL-17, TNF-α. Osteolytic mediator, e.g., RANK, RANKL, Wnt5a and proteinase enzymes, MMP-2, MMP-9, and Cathepsin-K were also expressed at higher level in peri-implantitis sites compared to control.

CONCLUSIONS

Peri-implantitis is associated with complex and different microbiota than healthy implants including bacteria, archaea, fungi, and virus. This difference in the microbiota could provoke higher inflammatory response and osteolytic activity. All of this could contribute to the physiopathology of peri-implantitis.

Impact of host genetics on gut microbiome: Take-home lessons from human and mouse studies

The intestinal microbiome has emerged as an important component involved in various diseases. Therefore, the interest in understanding the factors shaping its composition is growing. The gut microbiome, often defined as a complex trait, contains diverse components and its properties are determined by a combination of external and internal effects. Although much effort has been invested so far, it is still difficult to evaluate the extent to which human genetics shape the composition of the gut microbiota. However, in mouse studies, where the environmental factors are better controlled, the effect of the genetic background was significant. The purpose of this paper is to provide a current assessment of the role of human host genetics in shaping the gut microbiome composition. Despite the inconsistency of the reported results, it can be estimated that the genetic factor affects a portion of the microbiome. However, this effect is currently lower than the initial estimates, and it is difficult to separate the genetic influence from the environmental effect. Additionally, despite the differences between the microbial composition of humans and mice, results from mouse models can strengthen our knowledge of host genetics underlying the human gut microbial variation.

Searching for a Bacteriophage Lysin to Treat Corynebacterium bovis in Immunocompromised Mice

Corynebacterium bovis is the causative agent of Corynebacterium-associated hyperkeratosis in immunocompromised mice. The resulting skin pathology can be profound and can be associated with severe wasting, making the animals unsuitable for research. Although the administration of antibiotics is effective in resolving clinical symptoms, antibiotics do not eradicate the offending bacterium. Furthermore, antibiotic use may be contraindicated as it can affect tumor growth and is associated with Clostridioides difficile enterotoxemia in highly immunocompromised murine strains. Lysins, which are lytic enzymes obtained from bacteriophages, are novel antimicrobial agents for treating bacterial diseases. The advantage of lysins are its target specificity, with minimal off-target complications that could affect the host or the biology of the engrafted tumor. The aim of this study was to identify lysins active against C. bovis. Chemical activation of latent prophages by using mitomycin C in 3 C. bovis isolates did not cause bacteriophage induction as determined through plaque assays and transmission electron microscopy. As an alternative approach, 8 lysins associated with other bacterial species, including those from the closely related species C. falsenii, were tested for their lytic action against C. bovis but were unsuccessful. These findings were congruent with the previously reported genomic analysis of 21 C. bovis isolates, which failed to reveal bacteriophage sequences by using the PHAST and PHASTER web server tools. From these results, we suggest C. bovis is among those rare bacterial species devoid of lysogenic bacteriophages, thus making the identification of C. bovis-specific lysins more challenging. However, C. bovis may be a useful model organism for studying the effects of antiphage systems.

Untapped sponge microbiomes: structure specificity at host order and family levels

Sponges are complex holobionts in which the structure of the microbiome has seldom been characterized above the host species level. The hypothesis tested in this study is that the structure of the sponge microbiomes is specific to the host at the order and family levels. This was done by using 33 sponge species belonging to 19 families representing five orders. A combination of three primer sets covering the V1-V8 regions of the 16S rRNA gene provided a more comprehensive coverage of the microbiomes. Both the diversity and structure of sponge microbiomes were demonstrated to be highly specific to the host phylogeny at the order and family levels. There are always dominant operational taxonomic units (OTUs) (relative abundance >1%) shared between microbial communities of sponges within the same family or order, but these shared OTUs showed high levels of dissimilarity between different sponge families and orders. The unique OTUs for a particular sponge family or order could be regarded as their 'signature identity'. 70%-87% of these unique OTUs (class level) are unaffiliated and represent a vast resource of untapped microbiota. This study contributes to a deeper understanding on the concept of host-specificity of sponge microbiomes and highlights a hidden reservoir of sponge-associated microbial resources.

Combined Targeted and Non-targeted PCR Based Methods Reveal High Levels of Compliance in Probiotic Products Sold as Dietary Supplements in United States and Canada

Probiotics are defined as "live microorganisms that, when administered in adequate amounts, confer a health benefit on the host." The diverse health benefits have contributed to rapid increase in probiotic consumption and in the value of probiotic market, valued at USD 46 billion in 2019. For probiotics to be effective, the correct species/strains should be delivered viable in an adequate dose. The most commonly used methods for species/strain identification are DNA based methods including targeted and non-targeted methods (e.g., high-throughput sequencing, HTS). Using different DNA based methods, previous studies reported several cases of non-compliance in probiotic products. The objectives of this study are to evaluate levels of compliance in probiotic products (presence of all declared species/strains, absence of any contaminants or undeclared species, and meeting the declared minimum viable cell count) and to compare the performance of targeted and non-targeted methods in probiotic authentication. To the best of our knowledge, this is the largest study of its kind, testing 182 probiotic products, containing a total of 520 strains, collected from United States and Canada. Using species-specific assays, 11 species could not be detected in ten products. Missing species were Lactobacillus casei in seven products, Bifidobacterium longum and Bifidobacterium bifidum in one product, B. longum in one product while B. longum subsp. longum was mislabeled as B. longum subsp. infantis in another. Additionally, undeclared Bifidobacterium animalis subsp. lactis was detected in one product. Viable count was determined for 72 samples and was found to be lower than declared in five samples, including one product showing no viable cells. Overall, non-compliance was observed in 15 out of 182 products (8%). Additionally, undeclared species at relative abundance of ∼1-2% were found in 14 products using HTS, however, their presence could not be confirmed using species-specific assays. The results show that targeted PCR based methods enable species and strain level identification. The results also highlight the need to continue to develop strain-specific assays appropriate for use with multi-strain products. True strain-specific assays will enable strain authentication in both single-strain products and multi-strain products to ensure probiotic products meet the label claims and ensure probiotic efficacy.

Associations of Cervicovaginal Lactobacilli With High-Risk Human Papillomavirus Infection, Cervical Intraepithelial Neoplasia, and Cancer: A Systematic Review and Meta-Analysis

BACKGROUND

Vaginal dysbiosis characterized by depleted lactobacilli is usually correlated with human papillomavirus (HPV) infection and cervical carcinogenesis, but the effect of the Lactobacillus genus and represented species on this process remains unclear.

METHODS

PubMed, EMBASE, and CENTRAL databases were searched up to February 15, 2019. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using a fixed-effect model and Review Manager (version 5.3) for Mac.

RESULTS

Eleven studies comprising 1230 cases were included. Lactobacillus spp. was associated with the decreased detection of high-risk subtype (hr)HPV infection (OR = 0.64, 95% CI = 0.48-0.87, I2 = 6%), cervical intraepithelial neoplasia (CIN) (OR = 0.53, 95% CI = 0.34-0.83, I2 = 0%), and cervical cancer (CC) (OR = 0.12, 95% CI = 0.04-0.36, I2 = 0%). At the level of Lactobacillus species, Lactobacillus crispatus, but not Lactobacillus iners, was correlated with the decreased detection of hrHPV infection (OR = 0.49, 95% CI = 0.31-0.79, I2 = 10%) and CIN (OR = 0.50, 95% CI = 0.29-0.88, I2 = 0%).

CONCLUSIONS

Cervicovaginal Lactobacillus spp. is associated with the decreased detection of hrHPV infection, CIN, and CC; L. crispatus may be the critical protective factor.

Microbiome analysis of healthy and diseased sponges Lubomirskia baicalensis by using cell cultures of primmorphs

Endemic sponges (Demosponges, Lubomirskiidae) dominate the fauna of the littoral zone of Lake Baikal. These freshwater sponges live in symbiosis with diverse eukaryotes and prokaryotes, including chlorophyll-containing microalgae. Within the last 5 years, the incidence of sponge disease and mortality events in Lake Baikal has increased. The etiology and ecology of these events remain unknown, in part because of the lack of models to study sponge-microbe interactions. In this work, we tested the use of primmorph cell cultures of Lubomirskia baicalensis as a tool for investigating the microbiomes of sponges. We infected primmorphs, cultured in vitro, with samples from diseased sponges and observed, by microscopy, disease symptoms, including loss of green symbionts, associated with mass die-off events. Subsequent sequencing of 16S rRNA gene fragments revealed that the microbiome community of healthy sponge and primmorphs formed a group separate from the community of diseased sponges and infected primmorphs. This confirms the suitability of the primmorph cell culture as a model sponge system. We also discovered mass mortality of green symbionts (Chlorophyta) was associated with a shift in the microbial communities of sponges/primmorphs. Microbes in diseased sponges, and infected primmorphs, belonged mainly to the phyla Bacteroidetes and Proteobacteria and these families Flavobacteriaceae, Burkholderiaceae, and Moraxellaceae. Primmorphs cell culture may provide a model to study interactions between these bacteria and their host and elucidate the cause of mass mortality events.

FORENSIC: an Online Platform for Fecal Source Identification

Sewage overflows, agricultural runoff, and stormwater discharges introduce fecal pollution into surface waters. Distinguishing these sources is critical for evaluating water quality and formulating remediation strategies. With the falling costs of sequencing, microbial community-based water quality assessment tools are under development. However, their application is limited by the need to build reference libraries, which requires extensive sampling of sources and bioinformatic expertise. Here, we introduce FORest Enteric Source IdentifiCation (FORENSIC; https://forensic.sfs.uwm.edu/), an online, library-independent source tracking platform based on random forest classification and 16S rRNA gene amplicon sequences to identify in environmental samples common fecal contamination sources, including humans, domestic pets, and agricultural animals. FORENSIC relies on a broad reference signature database of Bacteroidales and Clostridiales, two predominant bacterial groups that have coevolved with their hosts. As a result, these groups demonstrate cohesive and reliable assemblage patterns within mammalian species or among species sharing the same diet/physiology. We created a scalable and extensible platform that we tested for global applicability using samples collected in distant geographic locations. This Web application offers a fast and intuitive approach for fecal source identification, particularly in sewage-contaminated waters.IMPORTANCE FORENSIC is an online platform to identify sources of fecal pollution without the need to create reference libraries. FORENSIC is based on the ability of random forest classification to extract cohesive source microbial signatures to create classifiers despite individual variability and to detect the signatures in environmental samples. We primarily focused on defining sewage signals, which are associated with a high human health risk in polluted waters. To test for fecal contamination sources, the platform only requires paired-end reads targeting the V4 or V6 regions of the 16S rRNA gene. We demonstrated that we could use V4V5 reads trimmed to the V4 positions to generate the reference signature. The systematic workflow we describe to create and validate the signatures could be applied to many disciplines. With the increasing gap between advancing technology and practical applications, this platform makes sequence-based water quality assessments accessible to the public health and water resource communities.

The characterization of bacterial communities of oropharynx microbiota in healthy children by combining culture techniques and sequencing of the 16S rRNA gene

The high incidence of bacterial respiratory infections has led to a focus on evaluating the human respiratory microbiome. Studies based on culture-based and molecular methods have shown an increase in the bacterial community that includes the bacterial phyla Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria in the oropharynx of healthy individuals. Therefore, recognizing this microbial compound and subsequently identifying those carriers of specific pathogens can be of great help in predicting future infections and their control. In this prospective study, we sought to characterize the bacterial communities of the respiratory microbiome in healthy children aged between 3 and 6 years old by combining both cultural techniques and sequencing of the 16S rRNA gene. Seventy-seven oropharynx samples using Dacron swabs were collected from 77 healthy children in the kindergartens of Ilam, Iran. Bacterial identification was performed by phenotypic methods and in house developed PCR-based sequencing (the V1-V9 hypervariable region of the bacterial 16S ribosomal RNA gene). In total, 346 bacterial isolates were characterized based on phenotypic and sequencing-based molecular methods. The 3 most predominant phyla were Firmicutes (74%), Proteobacteria (22%), and Actinobacteria (4%). At the level of the genus, Staphylococci (coagulase-positive and coagulase-negative) and Streptococci were dominant. Also, the most commonly identified potentially pathogenic colonisers were S. aureus (75%), Enterobacteriaceae spp. (40.1%), and A. baumannii (15.6%). The present study identified 3 phyla and 9 family of bacteria in the oropharyngeal microbiome. Remarkably, the presence of potential pathogenic bacteria in the nasopharynx of healthy children can predispose them to infectious diseases, and also frequent exposure to human respiratory bacterial pathogens are further risk factors.

The Gut Microbiome and Schizophrenia: The Current State of the Field and Clinical Applications

Schizophrenia is a debilitating psychiatric disorder, leading to both physical and social morbidity. Despite its importance, the etiology of schizophrenia remains poorly understood. Furthermore, its mainstream treatments fail to address all aspects of the disorder and are associated with significant side-effects. Recently, there has been growing interest in the relationship between the gut microbiome and mental health, including in schizophrenia. In this article, we review the existing evidence implicating dysbiosis in schizophrenia and discuss how the presumed dysbiosis could fit within known hypotheses of its pathogenesis, focusing on inflammation, tryptophan metabolites, and BDNF levels. We also evaluate the clinical potential of manipulating the gut microbiome with probiotics and prebiotics as adjunctive treatments in schizophrenia, based on existing clinical and pre-clinical studies. Overall, the current data showing microbiome alterations in schizophrenia are highly discrepant and insufficient to conclude whether microbiome changes are associated with increased risk of the disorder, or are simply the result of external factors or treatment. Despite some encouraging results of pro/prebiotic supplementation, there is also inconclusive evidence for their efficacy in schizophrenia. Thus, further research and more clinical trials are needed to test the validity of manipulating the gut microbiome to improve the treatment of this disorder.

Anterior Nares Diversity and Pathobionts Represent Sinus Microbiome in Chronic Rhinosinusitis

It is generally believed that the microbiome plays a role in the pathophysiology of chronic rhinosinusitis (CRS), though its exact contribution to disease development and severity remains unclear. Here, samples were collected from the anterior nares, nasopharynx, and maxillary and ethmoid sinuses of 190 CRS patients and from the anterior nares and nasopharynx of 100 controls. Microbial communities were analyzed by Illumina sequencing of the V4 region of 16S rRNA. The phenotype and patient characteristics were documented, and several serum inflammatory markers were measured. Our data indicate a rather strong continuity for the microbiome in the different upper respiratory tract (URT) niches in CRS patients, with the microbiome in the anterior nares being most similar to the sinus microbiome. Bacterial diversity was reduced in CRS patients without nasal polyps compared to that in the controls but not in CRS patients with nasal polyps. Statistically significant differences in the presence/absence or relative abundance of several taxa were found between the CRS patients and the healthy controls. Of these, Dolosigranulum pigrum was clearly more associated with URT samples from healthy subjects, while the Corynebacterium tuberculostearicum, Haemophilus influenzae/H. aegyptius, and Staphylococcus taxa were found to be potential pathobionts in CRS patients. However, CRS versus health as a predictor explained only 1 to 2% of the variance in the microbiome profiles in an adonis model. A history of functional endoscopic sinus surgery, age, and sex also showed a minor association. This study thus indicates that functional studies on the potential beneficial versus pathogenic activity of the different indicator taxa found here are needed to further understand the pathology of CRS and its different phenotypes. (This study has been registered at ClinicalTrials.gov under identifier NCT02933983.)IMPORTANCE There is a clear need to better understand the pathology and specific microbiome features in chronic rhinosinusitis patients, but little is known about the bacterial topography and continuity between the different niches of the upper respiratory tract. Our work showed that the anterior nares could be an important reservoir for potential sinus pathobionts. This has implications for the diagnosis, prevention, and treatment of CRS. In addition, we found a potential pathogenic role for the Corynebacterium tuberculostearicum, Haemophilus influenzae/H. aegyptius, and Staphylococcus taxa and a potential beneficial role for Dolosigranulum Finally, a decreased microbiome diversity was observed in patients with chronic rhinosinusitis without nasal polyps compared to that in healthy controls but not in chronic rhinosinusitis patients with nasal polyps. This suggests a potential role for the microbiome in disease development or progression of mainly this phenotype.

Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils

16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, no universal primer pair can target all bacteria and archaea, resulting in different primer pairs which may impact the diversity profile obtained. Here, we evaluated three pairs of high-throughput sequencing primers for characterizing archaeal communities from deep-sea sediments and permafrost soils. The results show that primer pair Arch519/Arch915 (V4-V5 regions) produced the highest alpha diversity estimates, followed by Arch349f/Arch806r (V3-V4 regions) and A751f/AU1204r (V5-V7 regions) in both sample types. The archaeal taxonomic compositions and the relative abundance estimates of archaeal communities are influenced by the primer pairs. Beta diversity of the archaeal community detected by the three primer pairs reveals that primer pairs Arch349f/Arch806r and Arch519f/Arch915r are biased toward detection of Halobacteriales, Methanobacteriales and MBG-E/Hydrothermarchaeota, whereas the primer pairs Arch519f/Arch915r and A751f/UA1204r are biased to detect MBG-B/Lokiarchaeota, and the primers pairs Arch349f/Arch806r and A751f/UA1204r are biased to detect Methanomicrobiales and Methanosarcinales. The data suggest that the alpha and beta diversities of archaeal communities as well as the community compositions are influenced by the primer pair choice. This finding provides researchers with valuable experimental insight for selection of appropriate archaeal primer pairs to characterize archaeal communities.

Saline wastewater treatment with purple phototrophic bacteria

Biological removal of organics, nitrogen and from saline wastewaters is adversely impacted by high salinity, which can be a major concern for treatment of industrial or domestic saline wastewater. In anaerobic treatment systems, sulfidogensis, especially when treating sulfate-rich saline wastewaters (e.g. seawater has 930 mgSO₄-S L^-1, or 2800 mg L^-1 as SO₄^2-) can cause additional biological, operational, and safety issues, due to H₂S toxicity. Here, the use of anaerobic purple phototrophic bacteria (PPB) is tested as mediator to treat high salinity domestic wastewater (NaCl), and marine wastewater (Red Sea Salt - high sulfate, potassium, etc.) in a continuous anaerobic infra-red photo bioreactor, operated over 372d. Saline adapted PPB simultaneously removed COD, nitrogen and phosphorus with biomass yields of 0.8 gCOD gCOD^-1. Batch activity tests found a broad optimum peak for saline adapted PPB between 30 and 70 mS cm^-1, and 50% reduced activity at 140 mS cm^-1 (3.5x seawater). For marine wastewater, high sulfate influent concentrations (770 mgSO₄-S L^-1) did not result in substantial H₂S production (<1.6 mgS L^-1) over 80 d. When irradiation was removed, sulfide rapidly rose to >90 mgS L^-1 and the process failed. The results indicate rapid adaptation to high-salt conditions (both NaCl and marine), and the capacity for PPB to form a combined wastewater treatment/resource recovery process, particularly for salty industrial wastewater.

Combining stable isotope analysis with DNA metabarcoding improves inferences of trophic ecology

Knowing what animals eat is fundamental to our ability to understand and manage biodiversity and ecosystems, but researchers often must rely on indirect methods to infer trophic position and food intake. Using an approach that combines evidence from stable isotope analysis and DNA metabarcoding, we assessed the diet and trophic position of Anthene usamba butterflies, for which there are no known direct observations of larval feeding. An earlier study that analyzed adults rather than caterpillars of A. usamba inferred that this butterfly was aphytophagous, but we found that the larval guts of A. usamba and two known herbivorous lycaenid species contain chloroplast 16S sequences. Moreover, chloroplast barcoding revealed high sequence similarity between chloroplasts found in A. usamba guts and the chloroplasts of the Vachellia drepanolobium trees on which the caterpillars live. Stable isotope analysis provided further evidence that A. usamba caterpillars feed on V. drepanolobium, and the possibilities of strict herbivory versus limited omnivory in this species are discussed. These results highlight the importance of combining multiple approaches and considering ontogeny when using stable isotopes to infer trophic ecology where direct observations are difficult or impossible.

Uncovering the hidden marine sponge microbiome by applying a multi-primer approach

Marine sponges (phylum Porifera) are hosts to microorganisms that make up to 40–60% of the mesohyl volume. The challenge is to characterise this microbial diversity more comprehensively. To accomplish this, a new method was for the first time proposed to obtain sequence coverage of all the variable regions of the 16S rRNA gene to analyze the amplicon-based microbiomes of four representative sponge species belonging to different orders. The five primer sets targeting nine variable regions of the 16S rRNA gene revealed a significant increase in microbiome coverage of 29.5% of phylum level OTUs and 35.5% class level OTUs compared to the community revealed by the commonly used V4 region-specific primer set alone. Among the resulting OTUs, 52.6% and 61.3% were unaffiliated, including candidate OTUs, at the phylum and class levels, respectively, which demonstrated a substantially superior performance in uncovering taxonomic ‘blind spots’. Overall, a more complete sponge microbiome profile was achieved by this multi-primer approach, given the significant improvement of microbial taxonomic coverage and the enhanced capacity to uncover novel microbial taxa. This multi-primer approach represents a fundamental and practical change from the conventional single primer set amplicon-based microbiome approach, and can be broadly applicable to other microbiome studies.

A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information

BACKGROUND

Subunits of ribosomal RNA genes (rDNAs) characterized by PCR-based protocols have been the proxy for studies in microbial taxonomy, phylogenetics, evolution and ecology. However, relevant factors have shown to interfere in the experimental outputs in a variety of systems. In this work, a 'theoretical' to 'actual' delta approach was applied to data on culturable mock bacterial communities (MBCs) to study the levels of losses in operational taxonomic units (OTUs) detectability. Computational and lab-bench strategies based on 16S rDNA amplification by 799F and U1492R primers were employed, using a fingerprinting method with highly improved detectability of fragments as a case-study tool. MBCs were of two major types: in silico MBCs, assembled with database-retrieved sequences, and in vitro MBCs, with AluI digestions of PCR data generated from culturable endophytes isolated from cacao trees.

RESULTS

Interfering factors for the 16 s rDNA amplifications, such as the type of template, direct and nested PCR, proportion of chloroplast DNA from a tropical plant source (Virola officinalis), and biased-amplification by the primers resulted in altered bacterial 16S rDNA amplification, both on MBCs and V. officinalis leaf-extracted DNA. For the theoretical data, the maximum number of fragments for in silico and in vitro cuts were not significantly different from each other. Primers' preferences for certain sequences were detected, depending on the MBCs' composition prior to PCR. The results indicated overall losses from 2.3 up to 8.2 times in the number of OTUs detected from actual AluI digestions of MBCs when compared to in silico and in vitro theoretical data.

CONCLUSIONS

Due to all those effects, the final amplification profile of the bacterial community assembled was remarkably simplified when compared to the expected number of detectable fragments known to be present in the MBC. From these findings, the scope of hypotheses generation and conclusions from experiments based on PCR amplifications of bacterial communities was discussed.