Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data

The genus Limnospira contains only two species both unable to produce microcystins: L. maxima and L. platensis comb. nov

Spirulina is the commercial name for edible cyanobacteria of the genus Limnospira. The taxonomy of this genus is confusing with four species distributed in two lineages. Furthermore, the species Limnospira fusiformis has been cited as toxic by potentially producing microcystins. Taxonomic ambiguity combined with suspected health concerns constitute a major issue for spirulina producers. In a collection of six cultivars and one ecotype, we identified strains of the two lineages through metagenetic and morphological analyses. We demonstrated that the genus Limnospira only comprises two distinct species according to genomic comparisons of three genomes obtained in this study and 19 reference genomes. We showed that the V3-V4 region of the 16S rRNA gene is sufficient to identify the genus Limnospira and to distinguish the two species. Toxinogenesis investigations on eleven genomes from each Limnospira species revealed no genes involved in cyanotoxin synthesis, reflecting the inability of this genus to produce microcystins.

Characterization of the microbiome of Aedes albopictus populations in different habitats from Spain and São Tomé

The mosquito microbiome significantly influences vector competence, including in Aedes albopictus, a globally invasive vector. Describing the microbiome and Wolbachia strains of Ae. albopictus from different regions can guide area-specific control strategies. Mosquito samples from Spain and São Tomé were analyzed using 16S rRNA gene sequencing and metagenomic sequencing. Wolbachia infection patterns were observed by sex and population. Female mosquitoes were blood-fed, a factor considered in analyzing their microbiota. Results revealed a dominance of dual Wolbachia infections, strains A and B, in the microbiome of both populations of Ae. albopictus, especially among females. Both populations shared a core microbiome, although 5 and 9 other genera were only present in Spain and São Tomé populations, respectively. Genera like Pelomonas and Nevskia were identified for the first time in Aedes mosquitoes. This study is the first to describe the Ae. albopictus bacteriome in Spain and São Tomé, offering insights for the development of targeted mosquito control strategies. Understanding the specific microbiome composition can help in designing more effective interventions, such as microbiome manipulation and Wolbachia-based approaches, to reduce vector competence and transmission potential of these mosquitoes.

Acanthamoebae as a protective reservoir for Pseudomonas aeruginosa in a clinical environment

BACKGROUND

Pseudomonas aeruginosa is a growing concern in healthcare-associated infections and poses significant risk to those with serious underlying health conditions. The antimicrobial resistance traits of the pathogen and ability to form biofilms make effective mitigation and disinfection strategies difficult. Added to this challenge is the role that free-living amoebae such as Acanthamoeba play in the detection, disinfection and transmission of P. aeruginosa. P. aeruginosa can survive intracellularly within amoebae, which has the potential to limit detectability and permit transmission into high-risk areas.

METHODS/FINDINGS

We screened for the presence of Acanthamoeba spp. and P. aeruginosa within a functioning general hospital in Scotland using a culture and molecular approach, noting their presence at several sites over a four-month period, particularly within floor drains connecting patient rooms. In addition, microbiome analysis revealed that amoebae harbour a unique microbial community comprised primarily of Pseudomonas spp. that were not readily detected using microbiome sequencing techniques on environmental swabs. Having demonstrated that both organisms were consistently present in hospital settings, we investigated the relationship between acanthamoeba and P. aeruginosa in the laboratory, showing that (i) acanthamoeba growth rate is increased in the presence of pseudomonas biofilms and viable pseudomonas persist within the amoebae and (ii) hydrogen peroxide-based disinfectants are significantly less effective against an isolate of P. aeruginosa in the presence of acanthamoeba than when the bacteria are incubated alone.

CONCLUSIONS

These findings suggest that amoebae, and other protists, can influence the detection and persistence of P. aeruginosa in high-risk areas and should be considered when implementing mitigation strategies.

The bacterial microbiome and resistome of house dust mites in Irish homes

Dust samples were collected from Irish homes. House Dust Mite and storage mites were separated from the dust. The microbiome and resistome of mites and originating dust were assessed using a culture-independent approach. The bacterial microbiome of mites and dust were predominantly populated by Staphylococci. There was a highly significant (P = 0.005; Spearman's rank test) correlation between the bacterial microbiome of mites and the dust. One-hundred and eighteen antimicrobial resistance genes (ARGs) were associated with mites and 176 with dust. Both contained ARGs encoding resistance for multi drug resistances, macrolide-lincosamide-streptogramin B, mobile genetic elements, Beta-lactam, Tetracycline and Aminoglycosides. By contrast, 15 ARGs were found for a laboratory-grown strain of Dermatophagoides pteronyssinus. A significant difference (P = 0.03; t test) was found in means between the resistome of mites and the household dust from which they emanated. No significant correlations (P = 0.23 and P = 0.22; Mantel test) were observed between the microbiome and resistome of mite and dust samples. There was not a significant difference (P = 0.54; t-test) between the means of ARGs for homes with and without a history of antibiotic use.

Distinct microdiversity of phosphate accumulating organisms (PAOs) between side-stream and conventional enhanced biological phosphorus removal (EBPR) systems with performance implications

Polyphosphate Accumulating Organisms (PAOs) microdiversity is a key factor to elucidate the mechanisms involved in the side-stream enhanced biological phosphorus removal (S2EBPR) systems, which has been shown to improve the process stability over conventional EBPR. However, fast, effective and cost-efficient methods to resolve PAO microdiversity in real-world activate sludge samples is still in absence. In this study, we applied oligotyping analysis following the regular 16S rRNA gene amplicon sequencing standard operation pipeline (SOP) to resolve subgenus-level PAO oligotypes, which cannot be achieved using traditional 16S rRNA sequencing SOP. The identified oligotype profiles of PAO-containing genera Ca. Accumulibacter, Tetrasphaera and Comamonas showed distinguished community-level differences across 12 water resource recovery facilities (WRRFs), which would not be revealed at the genus level. The WRRF-level differences were observed larger than the temporal differences in the same WRRF, indicating intrinsic sub-genus level microdiversity fingerprint between EBPR/S2EBPR systems. The identified oligotypes can be associated with known PAO clades phylogenetically, suggesting that oligotyping can suffice as a fast and cost-efficient approach for PAO microdiversity profiling. In addition, network analysis can be used to identify coexistence patterns between oligotypes with respect to EBPR/S2EBPR configurations and performance, enabling more detailed analysis between EBPR system performance and PAOs microdiversity. Correlation analyses between oligotype profiles and key EBPR performance parameters revealed potential different biological functional traits among these PAO species with P-removal performance implications.

Microbial Diversity of Soil in a Mediterranean Biodiversity Hotspot: Parque Nacional La Campana, Chile

Parque Nacional La Campana (PNLC) is recognized worldwide for its flora and fauna, rather than for its microbial richness. Our goal was to characterize the structure and composition of microbial communities (bacteria, archaea and fungi) and their relationship with the plant communities typical of PNLC, such as sclerophyllous forest, xerophytic shrubland, hygrophilous forest and dry sclerophyllous forest, distributed along topoclimatic variables, namely, exposure, elevation and slope. The plant ecosystems, the physical and chemical properties of organic matter and the soil microbial composition were characterized by massive sequencing (iTag-16S rRNA, V4 and ITS1-5F) from the DNA extracted from the soil surface (5 cm, n = 16). A contribution of environmental variables, particularly related to each location, is observed. Proteobacteria (35.43%), Actinobacteria (32.86%), Acidobacteria (10.07%), Ascomycota (76.11%) and Basidiomycota (15.62%) were the dominant phyla. The beta diversity (~80% in its axes) indicates that bacteria and archaea are linked to their plant categories, where the xerophytic shrub stands out with the most particular microbial community. More specifically, Crenarchaeote, Humicola and Mortierella were dominant in the sclerophyllous forest; Chloroflexi, Cyanobacteria and Alternaria in the xerophytic shrubland; Solicoccozyma in the dry sclerophyllous forest; and Cladophialophora in the hygrophilous forest. In conclusion, the structure and composition of the microbial consortia is characteristic of PNLC's vegetation, related to its topoclimatic variables, which suggests a strong association within the soil microbiome.

Persistent enrichment of multidrug-resistant Klebsiella in oral and nasal communities during long-term starvation

BACKGROUND

The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human populations via the environment, and they routinely possess clinically significant antibiotic resistance genes. Among these opportunistic pathogens, the Klebsiella genus stands out as a notable example, with its members frequently linked to nosocomial infections and multidrug resistance. As with many colonizing opportunistic pathogens, the essential transmission factors influencing the spread of Klebsiella species among both healthy and diseased individuals remain unclear.

RESULTS

Here, we explored a possible explanation by investigating the ability of oral and nasal Klebsiella species to outcompete their native microbial community members under in vitro starvation conditions, which could be analogous to external hospital environments or the microenvironment of mechanical ventilators. When K. pneumoniae and K. aerogenes were present within a healthy human oral or nasal sample, the bacterial community composition shifted dramatically under starvation conditions and typically became enriched in Klebsiella species. Furthermore, introducing K. pneumoniae exogenously into a native microbial community lacking K. pneumoniae, even at low inoculum, led to repeated enrichment under starvation. Precise monitoring of K. pneumoniae within these communities undergoing starvation indicated rapid initial growth and prolonged viability compared to other members of the microbiome. K. pneumoniae strains isolated from healthy individuals' oral and nasal cavities also exhibited resistance to multiple classes of antibiotics and were genetically similar to clinical and gut isolates. In addition, we found that in the absence of Klebsiella species, other understudied opportunistic pathogens, such as Peptostreptococcus, increased in relative abundance under starvation conditions.

CONCLUSIONS

Our findings establish an environmental and microbiome community circumstance that allows for the enrichment of Klebsiella species and other opportunistic pathogens. Klebsiella's enrichment may hinge on its ability to quickly outgrow other members of the microbiome. The ability to outcompete other commensal bacteria and to persist under harsh environmental conditions could be an important factor that contributes to enhanced transmission in both commensal and pathogenic contexts. Video Abstract.

No Evidence of Gut Microbiota Alteration in Psoriasis Patients Switching to Brodalumab after Loss of TNFα Inhibition Effect

Biological agents used to treat severe psoriasis may alter the gut microbiota, though current knowledge is limited. This study examines whether switching from TNFα inhibitors, from which patients had reduced or lost effect, to brodalumab, an IL-17 inhibitor, affects the gut microbiota in patients with psoriasis and how these changes correlate with the clinical variables of psoriasis severity and depressive symptoms. Fecal samples from patients were collected before the treatment switch and 12 weeks after the switch and were analyzed for the microbiota composition using next-generation sequencing targeting the V3-V5 region of the 16S rRNA gene, followed by bioinformatics analysis. No significant changes in overall gut microbiota composition were observed after the treatment switch, although individual variations in the Firmicutes/Bacteroidetes ratio were noted, and no significant correlations with clinical variables were found. These findings suggest that short-term changes in gut microbiota in patients with psoriasis are limited and that dysbiosis may be influenced by the interplay of various microbial populations rather than specific taxa. This study provides a foundation for further research into the effects of biological treatments on the gut microbiota in patients with psoriasis.

Niche-dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis

BACKGROUND

Most researches on sponge holobionts focus primarily on symbiotic microbes, yet data at the level of the sponge hologenome are still relatively scarce. Understanding of the sponge host and its microbial gene expression profiles and the host-microbes interplay in different niches represents a key aspect of sponge hologenome. Using the Hawaiian demosponge Mycale grandis in different niches as a model, i.e. on rocks, on the surface of coral Porites compressa, under alga Gracilaria salicornia, we compared the bacterial and fungal community structure, functional gene diversity, expression pattern and the host transcriptome by integrating open-format (deep sequencing) and closed-format (GeoChip microarray) high-throughput techniques.

RESULTS

Little inter-niche variation in bacterial and fungal phylogenetic diversity was detected for M. grandis in different niches, but a clear niche-dependent variability in the functional gene diversity and expression pattern of M. grandis host and its symbiotic microbiota was uncovered by GeoChip microarray and transcriptome analyses. Particularly, sponge host genes related to innate immunity and microbial recognition showed a strong correlation with the microbial symbionts' functional gene diversity and transcriptional richness in different niches. The cross-niche variability with respect to the symbiont functional gene diversity and the transcriptional richness of M. grandis holobiont putatively reflects the interplay of niche-specific selective pressure and the symbiont functional diversity.

CONCLUSIONS

Niche-dependent gene expression profiles of M. grandis hologenome and the host-microbes interplay were suggested though little inter-niche variation in bacterial and fungal diversity was detected, particularly the sponge innate immunity was found to be closely related to the symbiotic microbes. Altogether, these findings provide novel insights into the black box of one sponge holobiont in different niches at the hologenome level.

Comammox and unknown ammonia oxidizers contribute to nitrite accumulation in an integrated A-B stage process that incorporates side-stream EBPR (S2EBPR)

A novel integrated pilot-scale A-stage high rate activated sludge, B-stage short-cut biological nitrogen removal and side-stream enhanced biological phosphorus removal (A/B-shortcut N-S2EBPR) process for treating municipal wastewater was demonstrated with the aim to achieve simultaneous and carbon- and energy-efficient N and P removal. In this studied period, an average of 7.62 ± 2.17 mg-N/L nitrite accumulation was achieved through atypical partial nitrification without canonical known NOB out-selection. Network analysis confirms the central hub of microbial community as Nitrospira, which was one to two orders of magnitude higher than canonical aerobic oxidizing bacteria (AOB) in a B-stage nitrification tank. The contribution of comammox Nitrospira as AOB was evidenced by the increased amoB/nxr ratio and higher ammonia oxidation activity. Furthermore, oligotyping analysis of Nitrospira revealed two dominant sub-clusters (microdiveristy) within the Nitrospira. The relative abundance of oligotype II, which is phylogenetically close to Nitrospira_midas_s_31566, exhibited a positive correlation with nitrite accumulation in the same operational period, suggesting its role as comammox Nitrospira. Additionally, the phylogenetic investigation suggested that heterotrophic organisms from the family Comamonadacea and the order Rhodocyclaceae embedding ammonia monooxygenase and hydroxylamine oxidase may function as heterotrophic nitrifiers. This is the first study that elucidated the impact of integrating the S2EBPR on nitrifying populations with implications on short-cut N removal. The unique conditions in the side-stream reactor, such as low ORP, favorable VFA concentrations and composition, seemed to exert different selective forces on nitrifying populations from those in conventional biological nutrient removal processes. The results provide new insights for integrating EBPR with short-cut N removal process for mainstream wastewater treatment.

Exploring the modulatory role of bovine lactoferrin on the microbiome and the immune response in healthy and Shiga toxin-producing E. coli challenged weaned piglets

BACKGROUND

Post-weaned piglets suffer from F18+ Escherichia coli (E. coli) infections resulting in post-weaning diarrhoea or oedema disease. Frequently used management strategies, including colistin and zinc oxide, have contributed to the emergence and spread of antimicrobial resistance. Novel antimicrobials capable of directly interacting with pathogens and modulating the host immune responses are being investigated. Lactoferrin has shown promising results against porcine enterotoxigenic E. coli strains, both in vitro and in vivo.

RESULTS

We investigated the influence of bovine lactoferrin (bLF) on the microbiome of healthy and infected weaned piglets. Additionally, we assessed whether bLF influenced the immune responses upon Shiga toxin-producing E. coli (STEC) infection. Therefore, 2 in vivo trials were conducted: a microbiome trial and a challenge infection trial, using an F18+ STEC strain. BLF did not affect the α- and β-diversity. However, bLF groups showed a higher relative abundance (RA) for the Actinobacteria phylum and the Bifidobacterium genus in the ileal mucosa. When analysing the immune response upon infection, the STEC group exhibited a significant increase in F18-specific IgG serum levels, whereas this response was absent in the bLF group.

CONCLUSION

Taken together, the oral administration of bLF did not have a notable impact on the α- and β-diversity of the gut microbiome in weaned piglets. Nevertheless, it did increase the RA of the Actinobacteria phylum and Bifidobacterium genus, which have previously been shown to play an important role in maintaining gut homeostasis. Furthermore, bLF administration during STEC infection resulted in the absence of F18-specific serum IgG responses.

A single Prochlorococcus ecotype dominates the tropical Bay of Bengal with ultradian growth

The Bay of Bengal (BoB) spans >2.2 million km2 in the northeastern Indian Ocean and is bordered by dense populations that depend upon its resources. Over recent decades, a shift from larger phytoplankton to picoplankton has been reported, yet the abundance, activity, and composition of primary producer communities are not well-characterized. We analysed the BoB regions during the summer monsoon. Prochlorococcus ranged up to 3.14 × 105 cells mL-1 in the surface mixed layer, averaging 1.74 ± 0.46 × 105 in the upper 10 m and consistently higher than Synechococcus and eukaryotic phytoplankton. V1-V2 rRNA gene amplicon analyses showed the High Light II (HLII) ecotype formed 98 ± 1% of Prochlorococcus amplicons in surface waters, comprising six oligotypes, with the dominant oligotype accounting for 65 ± 4% of HLII. Diel sampling of a coherent water mass demonstrated evening onset of cell division and rapid Prochlorococcus growth between 1.5 and 3.1 div day-1, based on cell cycle analysis, as confirmed by abundance-based estimates of 2.1 div day-1. Accumulation of Prochlorococcus produced by ultradian growth was restricted by high loss rates. Alongside prior Arabian Sea and tropical Atlantic rates, our results indicate Prochlorococcus growth rates should be reevaluated with greater attention to latitudinal zones and influences on contributions to global primary production.

Revisiting the role of Acinetobacter spp. in side-stream enhanced biological phosphorus removal (S2EBPR) systems

We piloted the incorporation of side-stream enhanced biological phosphorus removal (S2EBPR) with A/B stage short-cut nitrogen removal processes to enable simultaneous carbon-energy-efficient nutrients removal. This unique configuration and system conditions exerted selective force on microbial populations distinct from those in conventional EBPR. Interestingly, effective P removal was achieved with the predominance of Acinetobacter (21.5 ± 0.1 %) with nearly negligible level of known conical PAOs (Ca. Accumulibacter and Tetrasphaera were 0.04 ± 0.10 % and 0.47 ± 0.32 %, respectively). Using a combination of techniques, such as fluorescence in situ hybridization (FISH) coupled with single cell Raman spectroscopy (SCRS), the metabolic tracing of Acinetobacter-like cells exerted PAO-like phenotypic profiling. In addition, comparative metagenomics analysis of the closely related Acinetobacter spp. revealed the EBPR relevant metabolic pathways. Further oligotyping analysis of 16s rRNA V4 region revealed sub-clusters (microdiversity) of the Acinetobacter and revealed that the sub-group (oligo type 1, identical (100 % alignment identity) hits from Acinetobacter_midas_s_49494, and Acinetobacter_midas_s_55652) correlated with EBPR activities parameters, provided strong evidence that the identified Acinetobacter most likely contributed to the overall P removal in our A/B-shortcut N-S2EBPR system. To the best of our knowledge, this is the first study to confirm the in situ EBPR activity of Acinetobacter using combined genomics and SCRS Raman techniques. Further research is needed to identify the specific taxon, and phenotype of the Acinetobacter that are responsible for the P-removal.

Role of KOH-activated biochar on promoting anaerobic digestion of biomass from Pennisetumgianteum

Pennisetum giganteum is a promising non-food crop feedstock for biogas production due to its high productivity and bio-methane potential. However, the accumulation of volatile fatty acids (VFA) usually restricts the conversion efficiency of P. giganteum biomass (PGB) during anaerobic digestion (AD). Here, the role of KOH-activated biochar (KB) in improving the AD efficiency of PGB and the related mechanisms were investigated in detail. The results revealed that KB exhibited excellent electrical conductivity, electron transfer capacity and specific capacitance, which might be related to the decrease in the electron transfer resistance after adding KB to the AD process. In addition, the KB addition not only reinforced metabolisms of energy and VFAs but also promoted the conversion of VFAs to methane, leading to a 52% increase in the methane production rate. Bioinformatics analysis showed that Smithella and Methanosaeta were key players in the KB-mediated AD process of PGB. The stimulatory effect of methanogenesis probably resulted from the establishment of direct interspecies electron transfer (DIET) between VFA-oxidizing acetogens (e.g., Smithella) and Methanosaeta. These findings provided a key step to improve the PGB-based AD process.

Population-level prokaryotic community structures associated with ferromanganese nodules in the Clarion-Clipperton Zone (Pacific Ocean) revealed by 16S rRNA gene amplicon sequencing

Although deep-sea ferromanganese nodules are a potential resource for exploitation, their formation mechanisms remain unclear. Several nodule-associated prokaryotic species have been identified by amplicon sequencing of 16S rRNA genes and are assumed to contribute to nodule formation. However, the recent development of amplicon sequence variant (ASV)-level monitoring revealed that closely related prokaryotic populations within an operational taxonomic unit often exhibit distinct ecological properties. Thus, conventional species-level monitoring might have overlooked nodule-specific populations when distinct populations of the same species were present in surrounding environments. Herein, we examined the prokaryotic community diversity of nodules and surrounding environments at the Clarion-Clipperton Zone in Japanese licensed areas by 16S rRNA gene amplicon sequencing with ASV-level resolution for three cruises from 2017 to 2019. Prokaryotic community composition and diversity were distinct by habitat type: nodule, nodule-surface mud, sediment, bottom water and water column. Most ASVs (~80%) were habitat-specific. We identified 178 nodule-associated ASVs and 41 ASVs associated with nodule-surface mud via linear discriminant effect size analysis. Moreover, several ASVs, such as members of SAR324 and Woeseia, were highly specific to nodules. These nodule-specific ASVs are promising targets for future investigation of the nodule formation process.

Persistent enrichment of multidrug resistant Klebsiella in oral and nasal communities during long-term starvation

The human oral and nasal cavities can act as reservoirs for opportunistic pathogens capable of causing acute infection. These microbes asymptomatically colonize the human oral and nasal cavities which facilitates transmission within human populations via the environment, and they routinely possess a clinically-significant antibiotic-resistance genes. Among these opportunistic pathogens, the Klebsiella genus stands out as a notable example, with its members frequently linked to nosocomial infections and multidrug resistance. As with many colonizing opportunistic pathogens, how Klebsiella transitions from an asymptomatic colonizer to a pathogen remains unclear. Here, we explored a possible explanation by investigating the ability of oral and nasal Klebsiella to outcompete their native microbial community members under in vitro starvation conditions, which could be analogous to external hospital environments. When Klebsiella was present within a healthy human oral or nasal sample, the bacterial community composition shifted dramatically under starvation conditions and typically became dominated by Klebsiella. Furthermore, introducing K. pneumoniae exogenously into a native microbial community lacking K. pneumoniae, even at low inoculum, led to repeated dominance under starvation. K.pneumoniae strains isolated from healthy individuals' oral and nasal cavities also exhibited resistance to multiple classes of antibiotics and were genetically similar to clinical and gut isolates. In addition, we found that in the absence of Klebsiella, other understudied opportunistic pathogens, such as Peptostreptococcus, dominate under starvation conditions. Our findings establish an environmental circumstance that allows for the outgrowth of Klebsiella and other opportunistic pathogens. The ability to outcompete other commensal bacteria and to persist under harsh environmental conditions may contribute to the colonization-to-infection transition of these opportunistic pathogens.

Microbiota Composition and Probiotics Supplementations on Sleep Quality-A Systematic Review and Meta-Analysis

The gut microbiota (GM) plays a crucial role in human health. The bidirectional interaction between GM and the central nervous system may occur via the microbiota-gut-brain axis, possibly regulating the sleep/wake cycle. Recent reports highlight associations between intestinal dysbiosis and sleep disorders, suggesting that probiotics could ameliorate this condition. However, data are poor and inconsistent. The aim of this quantitative metanalytic study is to assess the GM composition in sleep disturbances and evaluate probiotics' effectiveness for managing sleep disorders. A systematic review was carried out until July 2022 in online databases, limiting the literature research to human studies and English language articles. No significant GM diversity between patients with sleep disturbances versus healthy controls was found, revealed by α-diversity, while β-diversity is missing due to lack of proper reporting. However, probiotics supplementation significantly reduced the self-assessed parameter of sleep quality and disturbances Pittsburgh Sleep Quality Index (PSQI) score compared with the placebo. No difference in the Epworth Sleepiness Scale (ESS) score was found. While available data suggest that GM diversity is not related to sleep disturbances, probiotics administration strongly improves sleep quality as a subjective perception. However, heterogeneity of data reporting in the scientific literature should be considered as a limitation.

Immunogenetics, sylvatic plague and its vectors: insights from the pathogen reservoir Mastomys natalensis in Tanzania

Yersinia pestis is a historically important vector-borne pathogen causing plague in humans and other mammals. Contemporary zoonotic infections with Y. pestis still occur in sub-Saharan Africa, including Tanzania and Madagascar, but receive relatively little attention. Thus, the role of wildlife reservoirs in maintaining sylvatic plague and spillover risks to humans is largely unknown. The multimammate rodent Mastomys natalensis is the most abundant and widespread rodent in peri-domestic areas in Tanzania, where it plays a major role as a Y. pestis reservoir in endemic foci. Yet, how M. natalensis' immunogenetics contributes to the maintenance of plague has not been investigated to date. Here, we surveyed wild M. natalensis for Y. pestis vectors, i.e., fleas, and tested for the presence of antibodies against Y. pestis using enzyme-linked immunosorbent assays (ELISA) in areas known to be endemic or without previous records of Y. pestis in Tanzania. We characterized the allelic and functional (i.e., supertype) diversity of the major histocompatibility complex (MHC class II) of M. natalensis and investigated links to Y. pestis vectors and infections. We detected antibodies against Y. pestis in rodents inhabiting both endemic areas and areas considered non-endemic. Of the 111 nucleotide MHC alleles, only DRB*016 was associated with an increased infestation with the flea Xenopsylla. Surprisingly, we found no link between MHC alleles or supertypes and antibodies of Y. pestis. Our findings hint, however, at local adaptations towards Y. pestis vectors, an observation that more exhaustive sampling could unwind in the future.

Comparison of exoskeleton microbial communities of co-occurring native and invasive crayfish species

Host-associated microbial communities are an important determinant of individual fitness and have recently been highlighted as one of the factors influencing the success of invasive species. Invasive hosts introduce their microbes into the new environment, and then both the host and its associated microbes enter into a series of interactions with the native macroscopic and microscopic biota. As these processes are largely unexplored, we aimed to compare the exoskeletal microbial communities of co-occurring and phylogenetically related crayfish: the native narrow-clawed crayfish Pontastacus leptodactylus and the invasive signal crayfish Pacifastacus leniusculus from the recently invaded Korana River, Croatia. The results of high-throughput 16S rRNA sequencing showed that the exoskeletal microbiome of both species is very diverse, significantly influenced by the local environment and dominated by low abundance bacterial families from the phylum Proteobacteria. Furthermore, the exoskeletal microbiomes of the crayfish species differed significantly in the composition and abundance of Amplicon Sequence Variants (ASVs), suggesting that they are to some extent shaped by species-specific intrinsic factors, despite sharing a common habitat. However, over 95% of the bacterial genera associated with the exoskeleton were detected in the exoskeleton samples of both native and invasive crayfish. We paid particular attention to two known crayfish pathogens, Aphanomyces astaci and Saprolegnia parasitica, and find that both species carry low amounts of both pathogens. On the side, we find that a non-standard ddPCR protocol outperforms standard qPCR test for A. astaci under low concentration conditions. Taken together, our results indicate the possibility of bidirectional mixing and homogenisation of exoskeleton microbiome. As such, they can serve as a baseline in future detangling of the processes that act together to shape the microbiomes of co-occuring native and invasive congeners during biological invasions.

Seasonal shifts in community composition and proteome expression in a sulphur-cycling cyanobacterial mat

Seasonal changes in light and physicochemical conditions have strong impacts on cyanobacteria, but how they affect community structure, metabolism, and biogeochemistry of cyanobacterial mats remains unclear. Light may be particularly influential for cyanobacterial mats exposed to sulphide by altering the balance of oxygenic photosynthesis and sulphide-driven anoxygenic photosynthesis. We studied temporal shifts in irradiance, water chemistry, and community structure and function of microbial mats in the Middle Island Sinkhole (MIS), where anoxic and sulphate-rich groundwater provides habitat for cyanobacteria that conduct both oxygenic and anoxygenic photosynthesis. Seasonal changes in light and groundwater chemistry were accompanied by shifts in bacterial community composition, with a succession of dominant cyanobacteria from Phormidium to Planktothrix, and an increase in diatoms, sulphur-oxidizing bacteria, and sulphate-reducing bacteria from summer to autumn. Differential abundance of cyanobacterial light-harvesting proteins likely reflects a physiological response of cyanobacteria to light level. Beggiatoa sulphur oxidation proteins were more abundant in autumn. Correlated abundances of taxa through time suggest interactions between sulphur oxidizers and sulphate reducers, sulphate reducers and heterotrophs, and cyanobacteria and heterotrophs. These results support the conclusion that seasonal change, including light availability, has a strong influence on community composition and biogeochemical cycling of sulphur and O2 in cyanobacterial mats.

The Bay of Bengal exposes abundant photosynthetic picoplankton and newfound diversity along salinity-driven gradients

The Bay of Bengal (BoB) is a 2,600,000 km2 expanse in the Indian Ocean upon which many humans rely. However, the primary producers underpinning food chains here remain poorly characterized. We examined phytoplankton abundance and diversity along strong BoB latitudinal and vertical salinity gradients-which have low temperature variation (27-29°C) between the surface and subsurface chlorophyll maximum (SCM). In surface waters, Prochlorococcus averaged 11.7 ± 4.4 × 104  cells ml-1 , predominantly HLII, whereas LLII and 'rare' ecotypes, HLVI and LLVII, dominated in the SCM. Synechococcus averaged 8.4 ± 2.3 × 104  cells ml-1 in the surface, declined rapidly with depth, and population structure of dominant Clade II differed between surface and SCM; Clade X was notable at both depths. Across all sites, Ostreococcus Clade OII dominated SCM eukaryotes whereas communities differentiated strongly moving from Arabian Sea-influenced high salinity (southerly; prasinophytes) to freshwater-influenced low salinity (northerly; stramenopiles, specifically, diatoms, pelagophytes, and dictyochophytes, plus the prasinophyte Micromonas) surface waters. Eukaryotic phytoplankton peaked in the south (1.9 × 104  cells ml-1 , surface) where a novel Ostreococcus was revealed, named here Ostreococcus bengalensis. We expose dominance of a single picoeukaryote and hitherto 'rare' picocyanobacteria at depth in this complex ecosystem where studies suggest picoplankton are replacing larger phytoplankton due to climate change.

Global scale phylogeography of functional traits and microdiversity in Prochlorococcus

Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype's phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus.

Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination

16S rRNA gene sequencing is widely used to characterize human and environmental microbiomes. Sequencing at scale facilitates better powered studies but is limited by cost and time. We identified two areas in our 16S rRNA gene library preparation protocol where modifications could provide efficiency gains, including (1) pooling of multiple PCR amplifications per sample to reduce PCR drift and (2) manual preparation of mastermix to reduce liquid handling. Using nasal samples from healthy human participants and a serially diluted mock microbial community, we compared alpha and beta diversity, and compositional abundance where the PCR amplification was conducted in triplicate, duplicate or as a single reaction, and where manually prepared or premixed mastermix was used. One hundred and fifty-eight 16S rRNA gene sequencing libraries were prepared, including a replicate experiment. Comparing PCR pooling strategies, we found no significant difference in high-quality read counts and alpha diversity, and beta diversity by Bray-Curtis index clustered by replicate on principal coordinate analysis (PCoA) and non-metric dimensional scaling (NMDS) analysis. Choice of mastermix had no significant impact on high-quality read and alpha diversity, and beta diversity by Bray-Curtis index clustered by replicate in PCoA and NMDS analysis. Importantly, we observed contamination and variability of rare species (<0.01 %) across replicate experiments; the majority of contaminants were accounted for by removal of species present at <0.1 %, or were linked to reagents (including a primer stock). We demonstrate no requirement for pooling of PCR amplifications or manual preparation of PCR mastermix, resulting in a more efficient 16S rRNA gene PCR protocol.

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.

High-volume hybridoma sequencing on the NeuroMabSeq platform enables efficient generation of recombinant monoclonal antibodies and scFvs for neuroscience research

The Neuroscience Monoclonal Antibody Sequencing Initiative (NeuroMabSeq) is a concerted effort to determine and make publicly available hybridoma-derived sequences of monoclonal antibodies (mAbs) valuable to neuroscience research. Over 30 years of research and development efforts including those at the UC Davis/NIH NeuroMab Facility have resulted in the generation of a large collection of mouse mAbs validated for neuroscience research. To enhance dissemination and increase the utility of this valuable resource, we applied a high-throughput DNA sequencing approach to determine immunoglobulin heavy and light chain variable domain sequences from source hybridoma cells. The resultant set of sequences was made publicly available as a searchable DNA sequence database (neuromabseq.ucdavis.edu) for sharing, analysis and use in downstream applications. We enhanced the utility, transparency, and reproducibility of the existing mAb collection by using these sequences to develop recombinant mAbs. This enabled their subsequent engineering into alternate forms with distinct utility, including alternate modes of detection in multiplexed labeling, and as miniaturized single chain variable fragments or scFvs. The NeuroMabSeq website and database and the corresponding recombinant antibody collection together serve as a public DNA sequence repository of mouse mAb heavy and light chain variable domain sequences and as an open resource for enhancing dissemination and utility of this valuable collection of validated mAbs.

Toward Integrating EBPR and the Short-Cut Nitrogen Removal Process in a One-Stage System for Treating High-Strength Wastewater

Enhanced biological phosphorus removal (EBPR) is an economical and sustainable process for phosphorus removal from wastewater. Despite the widespread application of EBPR for low-strength domestic wastewater treatment, limited investigations have been conducted to apply EBPR to the high-strength wastewaters, particularly, the integration of EBPR and the short-cut nitrogen removal process in the one-stage system remains challenging. Herein, we reported a novel proof-of-concept demonstration of integrating EBPR and nitritation (oxidation of ammonium to nitrite) in a one-stage sequencing batch reactor to achieve simultaneous high-strength phosphorus and short-cut nitrogen removal. Excellent EBPR performance of effluent 0.8 ± 1.0 mg P/L and >99% removal efficiency was achieved fed with synthetic high-strength phosphorus wastewater. Long-term sludge acclimation proved that the dominant polyphosphate accumulating organisms (PAOs), Candidatus Accumulibacter, could evolve to a specific subtype that can tolerate the nitrite inhibition as revealed by operational taxonomic unit (OTU)-based oligotyping analysis. The EBPR kinetic and stoichiometric evaluations combined with the amplicon sequencing proved that the Candidatus Competibacter, as the dominant glycogen accumulating organisms (GAOs), could well coexist with PAOs (15.3-24.9% and 14.2-33.1%, respectively) and did not deteriorate the EBPR performance. The nitrification activity assessment, amplicon sequencing, and functional-based gene marker quantification verified that the unexpected nitrite accumulation (10.7-21.0 mg N/L) in the high-strength EBPR system was likely caused by the nitritation process, in which the nitrite-oxidizing bacteria (NOB) were successfully out-selected (<0.1% relative abundance). We hypothesized that the introduction of the anaerobic phase with high VFA concentrations could be the potential selection force for achieving nitritation based on the literature review and our preliminary batch tests. This study sheds light on developing a new feasible technical route for integrating EBPR with short-cut nitrogen removal for efficient high-strength wastewater treatment.

The respiratory microbiota and its impact on health and disease in dogs and cats: A One Health perspective

Healthy lungs were long thought of as sterile, with presence of bacteria identified by culture representing contamination. Recent advances in metagenomics have refuted this belief by detecting rich, diverse, and complex microbial communities in the healthy lower airways of many species, albeit at low concentrations. Although research has only begun to investigate causality and potential mechanisms, alterations in these microbial communities (known as dysbiosis) have been described in association with inflammatory, infectious, and neoplastic respiratory diseases in humans. Similar studies in dogs and cats are scarce. The microbial communities in the respiratory tract are linked to distant microbial communities such as in the gut (ie, the gut-lung axis), allowing interplay of microbes and microbial products in health and disease. This review summarizes considerations for studying local microbial communities, key features of the respiratory microbiota and its role in the gut-lung axis, current understanding of the healthy respiratory microbiota, and examples of dysbiosis in selected respiratory diseases of dogs and cats.

A streamlined pipeline based on HmmUFOtu for microbial community profiling using 16S rRNA amplicon sequencing

Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We present a streamlined pipeline that integrates FastP for read trimming, HmmUFOtu for operational taxonomic units (OTU) clustering, Vsearch for chimera checking, and Kraken2 for taxonomic assignment. To assess the pipeline's performance, we reprocessed two published stool datasets of normal Korean populations: one with 890 and the other with 1,462 independent samples. In the first dataset, HmmUFOtu retained 93.2% of over 104 million read pairs after quality trimming, discarding chimeric or unclassifiable reads, while DADA2, a commonly used ASV method, retained only 44.6% of the reads. Nonetheless, both methods yielded qualitatively similar β-diversity plots. For the second dataset, HmmUFOtu retained 89.2% of read pairs, while DADA2 retained a mere 18.4% of the reads. HmmUFOtu, being a closed-reference clustering method, facilitates merging separately processed datasets, with shared OTUs between the two datasets exhibiting a correlation coefficient of 0.92 in total abundance (log scale). While the first two dimensions of the β-diversity plot exhibited a cohesive mixture of the two datasets, the third dimension revealed the presence of a batch effect. Our comparative evaluation of ASV and OTU methods within this streamlined pipeline provides valuable insights into their performance when processing large-scale microbial 16S rRNA amplicon sequencing data. The strengths of HmmUFOtu and its potential for dataset merging are highlighted.

Emodin Inhibited Pathological Cardiac Hypertrophy in Response to Angiotensin-Induced Hypertension and Altered the Gut Microbiome

OBJECTIVE

Evidence suggests that food bioactives affect the epigenome to prevent pathological cardiac hypertrophy. Recently, we showed that emodin, an anthraquinone, attenuated pathological cardiac hypertrophy and histone deacetylase (HDAC) activity. However, we only examined the cardioprotective effects of emodin's parent compound and not those of emodin metabolites or of emodin-gut microbiome interactions. The microbiome has emerged as a key player in chronic diseases such as metabolic and cardiac disease. Thus, we hypothesized that emodin could reverse hypertension-induced changes in microbial communities.

METHODS

Normo- and hypertensive (angiotensin II) C57/BL6 female mice were randomly assigned to receive a vehicle (Veh; DMSO:PEG 1:1) or emodin (Emod; 30 mg/kg) for 14 days. Body weights were collected pre- and post-treatment, and blood pressure was assessed via tail cuff. At the study's end, the mice were euthanized and assessed for their heart weights. In addition, stool samples and cecal contents were collected to elucidate changes in the microbial populations using 16S rRNA sequencing. Lastly, the tissue was lysed, and RNA was isolated for qPCR. One-way ANOVA with Tukey's post hoc test was performed unless otherwise specified, and p < 0.05 was considered significant.

RESULTS

Emodin significantly attenuated cardiac hypertrophy in the female mice. No significant changes were observed in body weight or systolic blood pressure in response to hypertension or emodin. Lastly, analysis suggests that hypertension altered the microbiome in the cecum and cecal content, with additional evidence to support that emodin affects gut microbiota in the feces and colon.

CONCLUSIONS

Our data demonstrate that emodin attenuates pathological hypertrophy in female mice. Future research is needed to dissect if changes in the microbiome contributes to emodin-mediated attenuation in cardiac remodeling.

Home-field advantage affects the local adaptive interaction between Andropogon gerardii ecotypes and root-associated bacterial communities

Due to climate change, drought frequencies and severities are predicted to increase across the United States. Plant responses and adaptation to stresses depend on plant genetic and environmental factors. Understanding the effect of those factors on plant performance is required to predict species' responses to environmental change. We used reciprocal gardens planted with distinct regional ecotypes of the perennial grass Andropogon gerardii adapted to dry, mesic, and wet environments to characterize their rhizosphere communities using 16S rRNA metabarcode sequencing. Even though the local microbial pool was the main driver of these rhizosphere communities, the significant plant ecotypic effect highlighted active microbial recruitment in the rhizosphere, driven by ecotype or plant genetic background. Our data also suggest that ecotypes planted at their homesites were more successful in recruiting rhizosphere community members that were unique to the location. The link between the plants' homesite and the specific local microbes supported the "home field advantage" hypothesis. The unique homesite microbes may represent microbial specialists that are linked to plant stress responses. Furthermore, our data support ecotypic variation in the recruitment of congeneric but distinct bacterial variants, highlighting the nuanced plant ecotype effects on rhizosphere microbiome recruitment. These results improve our understanding of the complex plant host-soil microbe interactions and should facilitate further studies focused on exploring the functional potential of recruited microbes. Our study has the potential to aid in predicting grassland ecosystem responses to climate change and impact restoration management practices to promote grassland sustainability. IMPORTANCE In this study, we used reciprocal gardens located across a steep precipitation gradient to characterize rhizosphere communities of distinct dry, mesic, and wet regional ecotypes of the perennial grass Andropogon gerardii. We used 16S rRNA amplicon sequencing and focused oligotyping analysis and showed that even though location was the main driver of the microbial communities, ecotypes could potentially recruit distinct bacterial populations. We showed that different A. gerardii ecotypes were more successful in overall community recruitment and recruitment of microbes unique to the "home" environment, when growing at their "home site." We found evidence for "home-field advantage" interactions between the host and host-root-associated bacterial communities, and the capability of ecotypes to recruit specialized microbes that were potentially linked to plant stress responses. Our study aids in a better understanding of the factors that affect plant adaptation, improve management strategies, and predict grassland function under the changing climate.

The ecology of scale: impact of volume on coalescence and function in methanogenic communities

Engineered ecosystems span multiple volume scales, from a nano-scale to thousands of cubic metres. Even the largest industrial systems are tested in pilot scale facilities. But does scale affect outcomes? Here we look at comparing different size laboratory anaerobic fermentors to see if and how the volume of the community affects the outcome of community coalescence (combining multiple communities) on community composition and function. Our results show that there is an effect of scale on biogas production. Furthermore, we see a link between community evenness and volume, with smaller scale communities having higher evenness. Despite those differences, the overall patterns of community coalescence are very similar at all scales, with coalescence leading to levels of biogas production comparable with that of the best-performing component community. The increase in biogas with increasing volume plateaus, suggesting there is a volume where productivity stays stable over large volumes. Our findings are reassuring for ecologists studying large ecosystems and industries operating pilot scale facilities, as they support the validity of pilot scale studies in this field.

Photobacterium predominate the microbial communities of muscle of European plaice (Pleuronectes platessa) caught in the Norwegian sea independent of skin and gills microbiota, fishing season, and storage conditions

The aim of this study was to investigate seasonal variations (September, December and April) in the initial microbial communities of skin and gills' external mucosal tissues (EMT) and muscle of European plaice (Pleuronectes platessa). Moreover, a potential relationship between EMT and fresh muscle microbiota was examined. The microbial community succession in plaice muscle as a function of fishing season and storage conditions was also investigated. The selected seasons for the storage experiment were September and April. Investigated storage conditions were; fillets packaged in either vacuum or modified atmosphere (70 % CO2, 20 % N2, 10 % O2) and chilled/refrigerated conditions (4 °C). Whole fish stored on ice (0 °C) was selected as a commercial standard. Seasonal variations were detected in the initial microbial communities of EMT and plaice muscle. The highest microbial diversity was found in EMT and muscle of April-caught plaice, followed by December and September catch indicating the important role of environmental factors in shaping the initial EMT and muscle microbial communities. The EMT microbial communities were more diverse than fresh muscle samples. The low number of shared taxa between EMT and initial muscle microbial communities indicates that only a minor part of the muscle microbiota came from the EMT. Psychrobacter and Photobacterium were the predominant genera in the EMT microbial communities in all seasons. Photobacterium dominated the initial muscle microbial communities with a gradual seasonal reduction of its abundance from September to April. Storage time and storage conditions shaped a less diverse and distinct community compared to the fresh muscle. However, no clear separation was seen between the communities at the middle and end of storage time. Regardless of EMT microbiota, fishing season and storage conditions, Photobacterium dominated the microbial communities of stored muscle samples. The Photobacterium prevalence as the primary specific spoilage organism (SSO) could be attributed to its high relative abundance in the initial microbiota of muscle and its CO2-tolerance. The findings of this study indicate the important contribution of Photobacterium to the microbial spoilage of plaice. Thus, the development of innovative preservation techniques addressing the rapid growth of Photobacterium could contribute to the production of high-quality and shelf-stable convenient retail plaice products.

NeuroMabSeq: high volume acquisition, processing, and curation of hybridoma sequences and their use in generating recombinant monoclonal antibodies and scFvs for neuroscience research

The Neuroscience Monoclonal Antibody Sequencing Initiative (NeuroMabSeq) is a concerted effort to determine and make publicly available hybridoma-derived sequences of monoclonal antibodies (mAbs) valuable to neuroscience research. Over 30 years of research and development efforts including those at the UC Davis/NIH NeuroMab Facility have resulted in the generation of a large collection of mouse mAbs validated for neuroscience research. To enhance dissemination and increase the utility of this valuable resource, we applied a high-throughput DNA sequencing approach to determine immunoglobulin heavy and light chain variable domain sequences from source hybridoma cells. The resultant set of sequences was made publicly available as searchable DNA sequence database ( neuromabseq.ucdavis.edu ) for sharing, analysis and use in downstream applications. We enhanced the utility, transparency, and reproducibility of the existing mAb collection by using these sequences to develop recombinant mAbs. This enabled their subsequent engineering into alternate forms with distinct utility, including alternate modes of detection in multiplexed labeling, and as miniaturized single chain variable fragments or scFvs. The NeuroMabSeq website and database and the corresponding recombinant antibody collection together serve as a public DNA sequence repository of mouse mAb heavy and light chain variable domain sequences and as an open resource for enhancing dissemination and utility of this valuable collection of validated mAbs.

Microbial Diversity Biased Estimation Caused by Intragenomic Heterogeneity and Interspecific Conservation of 16S rRNA Genes

The 16S rRNA gene has been extensively used as a molecular marker to explore evolutionary relationships and profile microbial composition throughout various environments. Despite its convenience and prevalence, limitations are inevitable. Variable copy numbers, intragenomic heterogeneity, and low taxonomic resolution have caused biases in estimating microbial diversity. Here, analysis of 24,248 complete prokaryotic genomes indicated that the 16S rRNA gene copy number ranged from 1 to 37 in bacteria and 1 to 5 in archaea, and intragenomic heterogeneity was observed in 60% of prokaryotic genomes, most of which were below 1%. The overestimation of microbial diversity caused by intragenomic variation and the underestimation introduced by interspecific conservation were calculated when using full-length or partial 16S rRNA genes. Results showed that, at the 100% threshold, microbial diversity could be overestimated by as much as 156.5% when using the full-length gene. The V4 to V5 region-based analyses introduced the lowest overestimation rate (4.4%) but exhibited slightly lower species resolution than other variable regions under the 97% threshold. For different variable regions, appropriate thresholds rather than the canonical value 97% were proposed for minimizing the risk of splitting a single genome into multiple clusters and lumping together different species into the same cluster. This study has not only updated the 16S rRNA gene copy number and intragenomic variation information for the currently available prokaryotic genomes, but also elucidated the biases in estimating prokaryotic diversity with quantitative data, providing references for choosing amplified regions and clustering thresholds in microbial community surveys. IMPORTANCE Microbial diversity is typically analyzed using marker gene-based methods, of which 16S rRNA gene sequencing is the most widely used approach. However, obtaining an accurate estimation of microbial diversity remains a challenge, due to the intragenomic variation and low taxonomic resolution of 16S rRNA genes. Comprehensive examination of the bias in estimating such prokaryotic diversity using 16S rRNA genes within ever-increasing prokaryotic genomes highlights the importance of the choice of sequencing regions and clustering thresholds based on the specific research objectives.

Translational informatics for human microbiota: data resources, models and applications

With the rapid development of human intestinal microbiology and diverse microbiome-related studies and investigations, a large amount of data have been generated and accumulated. Meanwhile, different computational and bioinformatics models have been developed for pattern recognition and knowledge discovery using these data. Given the heterogeneity of these resources and models, we aimed to provide a landscape of the data resources, a comparison of the computational models and a summary of the translational informatics applied to microbiota data. We first review the existing databases, knowledge bases, knowledge graphs and standardizations of microbiome data. Then, the high-throughput sequencing techniques for the microbiome and the informatics tools for their analyses are compared. Finally, translational informatics for the microbiome, including biomarker discovery, personalized treatment and smart healthcare for complex diseases, are discussed.

Mitigating the inhibition of antibacterial agent chloroxylenol on nitrification system-The role of Rhodococcus ruber in a bioaugmentation system

The chloroxylenol (PCMX) degrading strain was successfully isolated from sludge and identified as Rhodococcus ruber (R. ruber). Afterwards, a bioaugmentation system was constructed by seeding R. ruber into nitrifying sludge to fasten degradation efficiency of highly toxic PCMX from wastewater. Results showed that R. ruber presented high PCMX-degrading performance under aerobic conditions, 25 °C, pH 7.0 and inoculum sizes of 4% (v/v). These optimized conditions were used in subsequent bioaugmentation experiment. In bioaugmentation system, R. ruber could detoxify nitrifiers by degrading PCMX, and the content of polysaccharide in extracellular polymeric substances increased. The quantitative polymerase chain reaction results exhibited that the absolute abundance of 16S rRNA gene and ammonia oxidizing bacteria (AOB) slightly elevated in bioaugmentation system. After analyzing the results of high-throughput sequencing, it was found that the loaded R. ruber can colonize successfully and turn into dominant strains in sludge system. Molecular docking simulation showed that PCMX had a weaker suppressed effect on AOB than nitrite oxidizing bacteria, and R. ruber can alleviate the adverse effect. This study could provide a novel strategy for potential application in reinforcement of PCMX removal in wastewater treatment.

Pulmonary Arterial Hypertension Patients Have a Proinflammatory Gut Microbiome and Altered Circulating Microbial Metabolites

Rationale: Inflammation drives pulmonary arterial hypertension (PAH). Gut dysbiosis causes immune dysregulation and systemic inflammation by altering circulating microbial metabolites; however, little is known about gut dysbiosis and microbial metabolites in PAH. Objectives: To characterize the gut microbiome and microbial metabolites in patients with PAH. Methods: We performed 16S ribosomal RNA gene and shotgun metagenomics sequencing on stool from patients with PAH, family control subjects, and healthy control subjects. We measured markers of inflammation, gut permeability, and microbial metabolites in plasma from patients with PAH, family control subjects, and healthy control subjects. Measurements and Main Results: The gut microbiome was less diverse in patients with PAH. Shannon diversity index correlated with measures of pulmonary vascular disease but not with right ventricular function. Patients with PAH had a distinct gut microbial signature at the phylogenetic level, with fewer copies of gut microbial genes that produce antiinflammatory short-chain fatty acids (SCFAs) and secondary bile acids and lower relative abundances of species encoding these genes. Consistent with the gut microbial changes, patients with PAH had relatively lower plasma concentrations of SCFAs and secondary bile acids. Patients with PAH also had enrichment of species with the microbial genes that encoded the proinflammatory microbial metabolite trimethylamine. The changes in the gut microbiome and circulating microbial metabolites between patients with PAH and family control subjects were not as substantial as the differences between patients with PAH and healthy control subjects. Conclusions: Patients with PAH have proinflammatory gut dysbiosis, in which lower circulating SCFAs and secondary bile acids may facilitate pulmonary vascular disease. These findings support investigating modulation of the gut microbiome as a potential treatment for PAH.

Amplicon-based next-generation sequencing for comparative analysis of root canal microbiome of teeth with primary and persistent/secondary endodontic infections

OBJECTIVES

To compare the root canal microbiome profiles of primary and persistent/secondary infections using high-throughput sequencing with the help of a reliable bioinformatics algorithm.

MATERIALS AND METHODS

Root canal samples of 10 teeth in the primary endodontic infection (PEI) group and 10 teeth in the persistent/secondary endodontic infection (SEI) group were included resulting in a total of 20 samples. After DNA extraction from the samples, sequencing was performed on the Illumina MiSeq platform. Pair-end Illumina reads were imported to QIIME 2; amplicon sequence variants (ASVs) generated by DADA2 were mapped to GreenGenes database. Weighted UniFrac distances were calculated and principal coordinates analysis (PCoA) was used to compare beta diversity patterns. The multiple response permutation procedure (MRPP), the analysis of similarities (ANOSIM), and permutational multivariate analysis of variance (adonis) were conducted for testing group differences. Linear discriminant analysis effect size (LEfSe) analysis was utilized to identify differentially abundant taxa between the groups. The linear discriminant analysis (LDA) score threshold was set to 4.0.

RESULTS

Within the Gram-negative facultative anaerobic Gammaproteobacteria class outgroup, two orders (Pasteurellales, Vibrionales) and two families (Pasteurellaceae, Vibrionaceae) were significantly more abundant in the PEI group, whereas Gram-positive bacteria, Actinomycetales order, and Gram-positive anaerobic taxa, one genus (Olsenella) and one species (Olsenella uli), were identified as significantly more abundant in the SEI group.

CONCLUSIONS

A few taxa were differentially abundant within either the PEI or SEI group.

CLINICAL RELEVANCE

Reliable bioinformatic tools are needed to define microbial profiles of endodontic infections. Based on a limited number of samples, no distinct variation was determined between the bacterial diversity of initial and recurrent endodontic infections.

Prevalence of Viral Frequency-Dependent Infection in Coastal Marine Prokaryotes Revealed Using Monthly Time Series Virome Analysis

Viruses infecting marine prokaryotes have a large impact on the diversity and dynamics of their hosts. Model systems suggest that viral infection is frequency dependent and constrained by the virus-host encounter rate. However, it is unclear whether frequency-dependent infection is pervasive among the abundant prokaryotic populations with different temporal dynamics. To address this question, we performed a comparison of prokaryotic and viral communities using 16S rRNA amplicon and virome sequencing based on samples collected monthly for 2 years at a Japanese coastal site, Osaka Bay. Concurrent seasonal shifts observed in prokaryotic and viral community dynamics indicated that the abundance of viruses correlated with that of their predicted host phyla (or classes). Cooccurrence network analysis between abundant prokaryotes and viruses revealed 6,423 cooccurring pairs, suggesting a tight coupling of host and viral abundances and their "one-to-many" correspondence. Although stable dominant species, such as SAR11, showed few cooccurring viruses, a fast succession of their viruses suggests that viruses infecting these populations changed continuously. Our results suggest that frequency-dependent viral infection prevails in coastal marine prokaryotes regardless of host taxa and temporal dynamics. IMPORTANCE There is little room for doubt that viral infection is prevalent among abundant marine prokaryotes regardless of their taxa or growth strategy. However, comprehensive evaluations of viral infections in natural prokaryotic communities are still technically difficult. In this study, we examined viral infection in abundant prokaryotes by monitoring the monthly dynamics of prokaryotic and viral communities at a eutrophic coastal site, Osaka Bay. We compared the community dynamics of viruses with those of their putative hosts based on genome-based in silico host prediction. We observed frequent cooccurrence among the predicted virus-host pairs, suggesting that viral infection is prevalent in abundant prokaryotes regardless of their taxa or temporal dynamics. This likely indicates that frequent lysis of the abundant prokaryotes via viral infection has a considerable contribution to the biogeochemical cycling and maintenance of prokaryotic community diversity.

Global scale phylogeography of functional traits and microdiversity in Prochlorococcus

Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenomically assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenomically assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype’s phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus .

The effects of dietary supplementation with mushroom or selenium enriched mushroom powders on the growth performance and intestinal health of post-weaned pigs

BACKGROUND

There is an urgent need to identify natural bioactive compounds that can enhance gastrointestinal health and promote pig growth performance in the absence of pharmacological levels of zinc oxide (ZnO). The objectives of this study were to: 1) compare the effects of mushroom powder supplemented with inorganic selenium (inSeMP) to mushroom powder enriched with organic selenium (orgSeMP) to pharmacological levels of ZnO on growth performance and faecal scores (FS) for the first 21 d post-weaning (Period 1); and 2) compare the molecular and microbial effects of inSeMP and orgSeMP in these pigs on d 39 post-weaning (Period 2).

METHODS

In Period 1, pigs (3 pigs/pen; 8 pens/treatment) were assigned to: (1) basal diet (control); (2) basal diet + zinc oxide (ZnO) (3100 mg/kg d 1-14, 1550 mg/kg d 15-21); (3) basal diet + mushroom powder supplemented with inorganic selenium (inSeMP) containing selenium (selenite) content of 0.3 mg/kg feed; (4) basal diet + mushroom powder enriched with organic selenium (orgSeMP) containing selenium (selenocysteine) content of 0.3 mg/kg feed. Mushroom powders were included at 6.5 g/kg of feed.

RESULTS

In Period 1, there was no effect of diets on average daily gain (ADG) and gain:feed (G:F) ratio (P > 0.05). The orgSeMP supplemented pigs had a lower average daily feed intake (ADFI) compared to all other groups (P < 0.05). The ZnO supplemented pigs had reduced FS compared to the basal and mushroom group, while the orgSeMP supplemented pigs had lower FS compared to the basal group during the 21 d experimental period (P < 0.05). In Period 2, there was no effect of diets on ADFI, ADG and G:F ratio (P > 0.05). The orgSeMP supplementation increased the caecal abundance of bacterial members of the Firmicutes and Bacteroidetes phylum, including Lactobacillus, Agathobacter, Roseburia, and Prevotella and decreased the abundance of Sporobacter compared to the basal group, while inSeMP increased the caecal abundance of Prevotella and decreased the caecal abundance of Sporobacter compared to the basal group (P < 0.05). Dietary supplementation with inSeMP increased expression of TLR4 and anti-inflammatory cytokine gene IL10 and decreased nutrient transporter gene FABP2 compared to the orgSeMP group (P < 0.05).

CONCLUSION

OrgSeMP is a novel and sustainable way to incorporate selenium and β-glucans into the diet of weaned pigs whilst improving FS and modulating the caecal microbiota.

Partial S(0)-driven autotrophic denitrification process facilitated the quick natural enrichment of anammox bacteria at room temperature

Anaerobic ammonium oxidation (anammox) is well-known to be an environmental and promising biotechnology. However, the natural enrichment of anammox bacteria is still a challenging topic. In this study, partial S(0)-driven autotrophic denitrification (PSAD) was developed to stably supply nitrite, and natural enrichment of anammox bacteria was rapidly realized in a single sequencing moving bed biofilm reactor at room temperature. With the initiation of PSAD, anammox bacteria spontaneously emerged within 12 days, and PSAD-anammox coupling system was realized successfully. And then, the influent concentration of ammonium continuously increased to the same concentration as the nitrate, and the mean total nitrogen removal efficiency reached 92.77 %, which was mainly contributed by anammox. Moreover, the coupling of PSAD and anammox reduced the risk of sulfate emissions. cDNA high throughput sequencing revealed that the relative abundance of Candidatus Brocadia and Thiobacillus reached 39.03 % and 13.48 % at the 88th day. Oligotyping analysis illustrated that GATTTAAT and GTCCCA were the dominant Ca. Brocadia and Thiobacillus oligotypes in PSAD-anammox coupling system, respectively. DNA-based stable isotope probing further deciphered that Thiobacillus was the actual performer of PSAD and supported the nitrite for anammox bacteria in PSAD-anammox coupling system. Overall, this work provided a new strategy to naturally enrich anammox bacteria.

Amelioration of cognitive impairment using epigallocatechin-3-gallate in ovariectomized mice fed a high-fat diet involves remodeling with Prevotella and Bifidobacteriales

Background: Estrogen deficiency and a high-fat diet (HFD) are both risk factors for Alzheimer's disease (AD). HFD can accelerate cognitive impairment in estrogen-deficient patients, but there is currently no effective treatment. Epigallocatechin-3-galate (EGCG) is widely studied for its anti-inflammatory, anti-cancer, and anti-neurodegeneration effects. Nevertheless, whether EGCG can ameliorate cognitive impairment in HFD-fed estrogen-deficient mice has not been studied. Methods and Results: Ovariectomized (OVX) mice fed an HFD (HFOVX) for 8 weeks experienced impaired object recognition and spatial memory, but this damage was significantly attenuated by the administration of EGCG at a dose of 45 mg/kg. Through 16S rRNA gene sequencing, we found that HFOVX changed the diversity and structure of the gut microbiota in mice, which could be restored with EGCG. Further analysis showed that HFOVX exposure not only resulted in a decrease of Alloprevotella in Bacteroidetes, Lactobacillaceae in Firmicutes, and Prevotella in Bacteroidetes but also in an increase of Bifidobacteriales in Actinobacteria. EGCG effectively reversed the decrease of Prevotella and inhibited the increase of Bifidobacteriales but had no effect on the decrease of Alloprevotella or Lactobacillaceae or on the increase of Enterorhabdus in HFOVX mice. Additionally, using Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we found that EGCG significantly reversed the five functional gut microbiota genes elevated by HFOVX, including iron complex transport system substrate-binding protein, iron complex transport system permease protein, 3-oxoacyl- [acyl-carrier protein] reductase, transketolase, and 8-oxo-dGTP diphosphatase. Conclusions: We concluded that EGCG improved cognitive impairment in mice with estrogen deficiency exacerbated by an HFD involved a rebuilding of the disrupted gut microbiota composition.

Spatio-temporal patterns of Synechococcus oligotypes in Moroccan lagoonal environments

Synechococcus are unicellular cyanobacteria susceptible to environmental fluctuations and can be used as bioindicators of eutrophication in marine ecosystems. We examined their distribution in two Moroccan lagoons, Marchica on the Mediterranean coast and Oualidia on the Atlantic, in the summers of 2014 and 2015 using 16S rRNA amplicon oligotyping. Synechococcus representatives recruited a higher number of reads from the 16S rRNA in Marchica in comparison to Oualidia. We identified 31 Synechococcus oligotypes that clustered into 10 clades with different distribution patterns. The Synechococcus community was mainly represented by oligotype 1 (clade III) in Marchica. Cooccurring clades IV and I had an important relative abundance in Marchica in the summer of 2014, which is unusual, as these clades are widespread in cold waters. Moreover, Clades VII and subcluster "5.3" formed a sizeable percentage of the Synechococcus community in Marchica. Notably, we found low Synechococcus sequence counts in the Atlantic Lagoon. These results showed that the relative abundance of Synechococcus reads is not constant over space and time and that rare members of the Synechococcus community did not follow a consistent pattern. Further studies are required to decipher Synechococcus dynamics and the impact of environmental parameters on their spatial and temporal distributions.

Effects of phytoplankton, viral communities, and warming on free-living and particle-associated marine prokaryotic community structure

Free-living and particle-associated marine prokaryotes have physiological, genomic, and phylogenetic differences, yet factors influencing their temporal dynamics remain poorly constrained. In this study, we quantify the entire microbial community composition monthly over several years, including viruses, prokaryotes, phytoplankton, and total protists, from the San-Pedro Ocean Time-series using ribosomal RNA sequencing and viral metagenomics. Canonical analyses show that in addition to physicochemical factors, the double-stranded DNA viral community is the strongest factor predicting free-living prokaryotes, explaining 28% of variability, whereas the phytoplankton (via chloroplast 16S rRNA) community is strongest with particle-associated prokaryotes, explaining 31% of variability. Unexpectedly, protist community explains little variability. Our findings suggest that biotic interactions are significant determinants of the temporal dynamics of prokaryotes, and the relative importance of specific interactions varies depending on lifestyles. Also, warming influenced the prokaryotic community, which largely remained oligotrophic summer-like throughout 2014-15, with cyanobacterial populations shifting from cold-water ecotypes to warm-water ecotypes.

High resolution 16S rRNA gene Next Generation Sequencing study of brain areas associated with Alzheimer's and Parkinson's disease

Introduction

Alzheimer's (AD) and Parkinson's disease (PD) are neurodegenerative conditions characterized by incremental deposition of β-amyloid (Aβ) and α-synuclein in AD and PD brain, respectively, in relatively conserved patterns. Both are associated with neuroinflammation, with a proposed microbial component for disease initiation and/or progression. Notably, Aβ and α-synuclein have been shown to possess antimicrobial properties. There is evidence for bacterial presence within the brain, including the oral pathobiont Porphyromonas gingivalis, with cognitive impairment and brain pathology being linked to periodontal (gum) disease and gut dysbiosis.

Methods

Here, we use high resolution 16S rRNA PCR-based Next Generation Sequencing (16SNGS) to characterize bacterial composition in brain areas associated with the early, intermediate and late-stage of the diseases.

Results and discussion

This study reveals the widespread presence of bacteria in areas of the brain associated with AD and PD pathology, with distinctly different bacterial profiles in blood and brain. Brain area profiles were overall somewhat similar, predominantly oral, with some bacteria subgingival and oronasal in origin, and relatively comparable profiles in AD and PD brain. However, brain areas associated with early disease development, such as the locus coeruleus, were substantially different in bacterial DNA content compared to areas affected later in disease etiology.

Methods of Identifying Gordonia Strains in Clinical Samples

Gordonia spp. are members of the family Gordoniacea in the suborder Corynebacteriales; their habitat, in most cases, is soil. Many representatives of this genus are human or veterinary pathogens. The main cause of the lack of a standardized approach to dealing with infections caused by Gordonia is their erroneous identification and little information regarding their susceptibility to antimicrobial drugs. This review presents the most common methods for identifying Gordonia strains, including modern approaches for identifying a species. The main prospects and future directions of this field of knowledge are briefly presented.

Influence of short and long term processes on SAR11 communities in open ocean and coastal systems

SAR11 bacteria dominate the surface ocean and are major players in converting fixed carbon back to atmospheric carbon dioxide. The SAR11 clade is comprised of niche-specialized ecotypes that display distinctive spatiotemporal transitions. We analyzed SAR11 ecotype seasonality in two long-term 16S rRNA amplicon time series representing different North Atlantic regimes: the Sargasso Sea (subtropical ocean-gyre; BATS) and the temperate coastal Western English Channel (WEC). Using phylogenetically resolved amplicon sequence variants (ASVs), we evaluated seasonal environmental constraints on SAR11 ecotype periodicity. Despite large differences in temperature and nutrient availability between the two sites, at both SAR11 succession was defined by summer and winter clusters of ASVs. The summer cluster was dominated by ecotype Ia.3 in both sites. Winter clusters were dominated by ecotypes Ib and IIa.A at BATS and Ia.1 and IIa.B at WEC. A 2-year weekly analysis within the WEC time series showed that the response of SAR11 communities to short-term environmental fluctuations was variable. In 2016, community shifts were abrupt and synchronized to environmental shifts. However, in 2015, changes were gradual and decoupled from environmental fluctuations, likely due to increased mixing from strong winds. We demonstrate that interannual weather variability disturb the pace of SAR11 seasonal progression.

Maternal supplementation with a casein hydrolysate and yeast beta-glucan from late gestation through lactation improves gastrointestinal health of piglets at weaning

Improving maternal nutrition during pregnancy/lactation is a promising strategy to maximise the intestinal health of piglets undergoing abrupt weaning under commercial production conditions. This experiment investigated the effects of maternal supplementation of a casein hydrolysate and yeast β-glucan (CH-YBG) from day 83 of gestation until weaning (day 28) on sow faecal microbial populations and measures of piglet gastrointestinal health parameters at weaning. Sows (n = 10 sows/group) were assigned to: (1) control diet, and (2) control diet + CH-YBG. Maternal supplementation increased the abundance of the phylum Firmicutes, including members Lactobacillus in the sows faeces, with a concomitant increase in the caecal abundance of Lactobacillus in the weaned piglets compared to the controls. Piglets weaned from the supplemented sows had increased villus height in the duodenum (P < 0.05) and increased villus height to crypt depth ratio in the jejunum, as well as a decreased expression of the proinflammatory cytokine genes (IL6/TNF/TGFB), the tight junction gene CLDN3 and the mucin gene MUC2 in the duodenum/jejunum compared to the controls (P < 0.05). In conclusion, maternal CH-YBG supplementation during pregnancy/lactation improved microbial, structural, and inflammatory measures of gastrointestinal health of piglets at weaning. This is a promising strategy to alleviate the challenges that occur with early abrupt weaning in commercial pig production.