Abundance Of Several Taxa Research Articles

The Gut Microbiota Profile in Children with Prader-Willi Syndrome.

Although gut microbiota has been suggested to play a role in disease phenotypes of Prader–Willi syndrome (PWS), little is known about its composition in affected children and how it relates to hyperphagia. This cross-sectional study aimed to characterize the gut bacterial and fungal communities of children with PWS, and to determine associations with hyperphagia. Fecal samples were collected from 25 children with PWS and 25 age-, sex-, and body mass index-matched controls. Dietary intake data, hyperphagia scores, and relevant clinical information were also obtained. Fecal bacterial and fungal communities were characterized by 16S rRNA and ITS2 sequencing, respectively. Overall bacterial α-diversity and compositions of PWS were not different from those of the controls, but 13 bacterial genera were identified to be differentially abundant. Interestingly, the fungal community, as well as specific genera, were different between PWS and controls. The majority of the variation in the gut microbiota was not attributed to differences in dietary intake or the impact of genotype. Hyperphagia scores were associated with fungal α-diversity and relative abundance of several taxa, such as Staphylococcus, Clostridium, SMB53, and Candida. Further longitudinal studies correlating changes in the microbiome with the degree of hyperphagia and studies integrating multi-omics data are warranted.

Treatment with Subcritical Water-Hydrolyzed Citrus Pectin Ameliorated Cyclophosphamide-Induced Immunosuppression and Modulated Gut Microbiota Composition in ICR Mice.

Subcritical water can effectively hydrolyze pectin into smaller molecules while still maintaining its functional regions. Pectic heteropolysaccharide can mediate immune regulation; however, the possible effects of subcritical water-hydrolyzed citrus pectin (SCP) on the immune response remain unclear. Therefore, the effects of SCP on immunomodulatory functions and intestinal microbial dysbiosis were investigated using a cyclophosphamide-induced immunosuppressed mouse model. In this research, immunosuppressed ICR mice were administrated with SCP at dosages of 300/600/1200 mg/kg.bw by oral gavage, and body weight, immune organ indexes, cytokines, and gut microbiota were determined. The results showed that subcritical water treatment decreased the molecular mass and increased the content of galacturonic acid in citrus pectin hydrolysates. Meanwhile, the treatment with SCP improved immunoregulatory functional properties and bioactivities over the original citrus pectin. For example, SCP protected immune organs (accelerated recovery of immune organ indexes) and significantly enhanced the expression of immune-related cytokines (IL-2, IL-6, IFN-γ, and TNF-α). The results of the 16S rDNA sequencing analysis on an IlluminaMiSeq platform showed that SCP normalized Cy-induced gut dysbiosis. SCP ameliorated Cy-dependent changes in the relative abundance of several taxa, shifting the balance back to normal status (e.g., SCP increased beneficial Muribaculaceae, Ruminococcaceae, Bacteroidaceae, and Prevotellaceae while decreasing pathogenic Brevundimonas and Streptococcus). The results of this study suggest an innovative application of citrus pectin as an immunomodulator.

Influence of Helicobacter pylori Infection and Atrophic Gastritis on the Gut Microbiota in a Japanese Population

Background: Although infection with Helicobacter pylori and subsequent atrophic gastritis modulate the gastric conditions, their relationship with the gut microbiota in ­Japanese population has not been clearly characterized. Methods: A cohort of 1,123 subjects who participated in a health survey was studied. Infection of H. pylori was defined by both serum antibody and stool antigen test. The presence and severity of atrophic gastritis were defined by serum levels of pepsinogens. The relative abundance of each bacterial species in fecal samples was calculated by using 16S ribosomal RNA amplification, and the composition ratios of bacterial taxa were evaluated using propensity score matching. Results: The abundance of 3 orders, 4 families, and 4 genera was significantly higher in H. pylori-infected subjects than in noninfected subjects (false discovery rate [FDR] <0.05). In H. pylori-infected subjects with severe atrophic gastritis, the abundance of the class Bacilli, order Lactobacillales, family Streptococcaceae, and genus Streptococcus was significantly higher than that in H. pylori-infected subjects without atrophic gastritis (FDR < 0.05). Conclusions: A significant increase in the relative abundance of several taxa was observed in gut microbiota of Japanese subjects with H. pylori infection. Among the subjects with severe atrophic gastritis, the increase in the genus Streptococcus is a remarkable characteristic.

Temporal variation in indoor transfer of dirt-associated environmental bacteria in agricultural and urban areas

An agricultural environment and exposure to diverse environmental microbiota has been suggested to confer protection against immune-mediated disorders. As an agricultural environment may have a protective role, it is crucial to determine whether the limiting factors in the transfer of environmental microbiota indoors are the same in the agricultural and urban environments. We explored how sampling month, garden diversity and animal ownership affected the indoor-transfer of environmental microbial community. We collected litter from standardized doormats used for 2 weeks in June and August 2015 and February 2016 and identified bacterial phylotypes using 16S rRNA Illumina MiSeq sequencing. In February, the diversity and richness of the whole bacterial community and the relative abundance of environment-associated taxa were reduced, whereas human-associated taxa and genera containing opportunistic pathogens were enriched in the doormats. In summer, the relative abundances of several taxa associated previously with beneficial health effects were higher, particularly in agricultural areas. Surprisingly, the importance of vegetation on doormat microbiota was more observable in February, which may have resulted from snow cover that prevented contact with microbes in soil. Animal ownership increased the prevalence of genera Bacteroides and Acinetobacter in rural doormats. These findings underline the roles of season, living environment and lifestyle in the temporal variations in the environmental microbial community carried indoors. As reduced contact with diverse microbiota is a potential reason for immune system dysfunction, the results may have important implications in the etiology of immune-mediated, non-communicable diseases.

Microbial Diversity in Bulk and Rhizosphere Soil of Ranunculus glacialis Along a High-Alpine Altitudinal Gradient.

Serving as “natural laboratories”, altitudinal gradients can be used to study changes in the distribution of microorganisms in response to changing environmental conditions that typically occur over short geographical distances. Besides, rhizosphere zones of plants are known to be hot-spots for microbial diversity and to contain different microbial communities when compared with surrounding bulk soil. To discriminate the effects of altitude and plants, we investigated the microbial communities in the rhizosphere of Ranunculus glacialis and bulk soil along a high-alpine altitudinal gradient (2,600–3,400 m a.s.l.). The research area of this study was Mount (Mt.) “Schrankogel” in the Central Alps of Tyrol (Austria). Our results point to significantly different microbial diversities and community compositions in the different altitudinal belts. In the case of prokaryotes, environmental parameters could explain 41% of the total variation of soil communities, with pH and temperature being the strongest influencing factors. Comparing the effects derived from fraction (bulk vs. rhizosphere soil) and environmental factors, the effects of the roots of R. glacialis accounted for about one third of the explained variation. Fungal communities on the other hand were nearly exclusively influenced by environmental parameters accounting for 37.4% of the total variation. Both, for altitudinal zones as well as for bulk and rhizosphere fractions a couple of very specific biomarker taxa could be identified. Generally, the patterns of abundance of several taxa did not follow a steady increased or decreased trend along the altitudinal gradient but in many cases a maximal or minimal occurrence was established at mid-altitudes (3,000–3,100 m). This mid-altitudinal zone is a transition zone (the so-called alpine-nival ecotone) between the (lower) alpine grassland/tundra zone and the (upper) sparsely vegetated nival zone and was shown to correspond with the summer snow line. Climate change and the associated increase in temperature will shift this transition zone and thus, might also shift the described microbial patterns and biomarkers.

Characterization of the non-glandular gastric region microbiota in Helicobacter suis-infected versus non-infected pigs identifies a potential role for Fusobacterium gastrosuis in gastric ulceration

Helicobacter suis has been associated with development of gastric ulcers in the non-glandular part of the porcine stomach, possibly by affecting gastric acid secretion and altering the gastric microbiota. Fusobacterium gastrosuis is highly abundant in the gastric microbiota of H. suis-infected pigs and it was hypothesized that this micro-organism could play a role in the development of gastric ulceration. The aim of this study was to obtain further insights in the influence of a naturally acquired H. suis infection on the microbiota of the non-glandular part of the porcine stomach and in the pathogenic potential of F. gastrosuis. Infection with H. suis influenced the relative abundance of several taxa at phylum, family, genus and species level. H. suis-infected pigs showed a significantly higher colonization rate of F. gastrosuis in the non-glandular gastric region compared to non-infected pigs. In vitro, viable F. gastrosuis strains as well as their lysate induced death of both gastric and oesophageal epithelial cell lines. These gastric cell death inducing bacterial components were heat-labile. Genomic analysis revealed that genes are present in the F. gastrosuis genome with sequence similarity to genes described in other Fusobacterium spp. that encode factors involved in adhesion, invasion and induction of cell death as well as in immune evasion. We hypothesize that, in a gastric environment altered by H. suis, colonization and invasion of the non-glandular porcine stomach region and production of epithelial cell death inducing metabolites by F. gastrosuis, play a role in gastric ulceration.

Social Stress Affects Colonic Inflammation, the Gut Microbiome, and Short-chain Fatty Acid Levels and Receptors.

Gastrointestinal disorders, such as inflammatory bowel diseases (IBDs) and functional gastrointestinal disorders (FGIDs), involve disrupted homeostatic interactions between the microbiota and the host. Both disorders are worsened during stress, and in laboratory mice, stress exposure has been shown to change the composition of the gut microbiome. Stress-induced changes to the microbiome exacerbate intestinal inflammation and alter intestinal motility in mice. It is, however, not yet known whether microbiota-derived short-chain fatty acids (butyrate, propionate, and acetate) and their receptors contribute to this effect. Mice were exposed to a social disruption stress, or left undisturbed as a control. After the first stress exposure, mice were orally challenged with Citrobacter rodentium or with vehicle. The levels of short-chain fatty acids (SCFAs) were measured using gas chromatography-mass spectrometry. SCFA receptors were measured via real-time polymerase chain reaction. Microbial community composition was assessed using 16S rRNA gene sequencing. Stress exposure reduced colonic SCFA levels. Stress exposure and C rodentium, however, significantly increased SCFA levels and changed the expression of SCFA receptors. The levels of SCFAs did not correlate with the severity of colonic inflammation, but the colonic expression of the SCFA receptor GPR41 was positively associated with inflammatory cytokines and colonic histopathology scores. The relative abundances of several taxa of colonic bacteria were significantly changed by stress exposure, including SCFA producers. Social stress can have a significant effect on infection-induced colonic inflammation, and stress-induced changes in microbial-produced metabolites and their receptors may be involved.

Meta‐analysis of management effects on biodiversity in plantation and secondary forests of Japan

Conservation of temperate forest biodiversity has historically focused on natural old‐growth. Less than 3% of the world's temperate forests remain unmodified by humans, however, and much of temperate‐forest biodiversity is held in the predominating planted and secondary forests. Japan provides a widely applicable model for examining how to maximize biodiversity in managed temperate forests, because of its richness of forestry research generated from its vast forest area, albeit largely in Japanese, and the wide practice of its dominant management interventions across the northern temperate zone. Management for plantations includes thinning, extended rotation cycles and clear‐cutting. For secondary forests regenerating from past clearance, traditional management varies in its intensities, from clear‐cutting as coppices to small‐scale understory clearance. Here we provide a first synthesis of published research on biodiversity in planted and secondary forests of Japan, relevant to management of these types of forest in northern temperate regions. Systematic review and meta‐analyses of papers published in English and Japanese quantified management impacts on species richness and abundance of several taxa, in relation to moderator variables including stand age and management intensity. Plantation thinning substantially increases the richness and abundance of several taxa. Effect sizes decline with time since thinning for the abundance of regenerating saplings and seedlings, necessitating repeated thinning treatments every 6 years to sustain this positive effect. Taxonomic groups exhibit variable relationships with stand age in both planted and secondary forests, indicating a need to include both young and old forest stands in managed forest mosaics. We find an insufficient evidence base is available to allow for a meaningful synthesis of low‐intensity management effects in historically managed secondary forests, with studies varying widely in scale and reported outcomes. We outline an agenda for the research community to achieve a systematic evaluation of scale‐dependent effects of traditional forest management on biodiversity.

Meta-analysis of management effects on biodiversity in plantation and secondary forests of Japan.

Conservation of temperate forest biodiversity has historically focused on natural old‐growth. Less than 3% of the world's temperate forests remain unmodified by humans, however, and much of temperate‐forest biodiversity is held in the predominating planted and secondary forests. Japan provides a widely applicable model for examining how to maximize biodiversity in managed temperate forests, because of its richness of forestry research generated from its vast forest area, albeit largely in Japanese, and the wide practice of its dominant management interventions across the northern temperate zone. Management for plantations includes thinning, extended rotation cycles and clear‐cutting. For secondary forests regenerating from past clearance, traditional management varies in its intensities, from clear‐cutting as coppices to small‐scale understory clearance. Here we provide a first synthesis of published research on biodiversity in planted and secondary forests of Japan, relevant to management of these types of forest in northern temperate regions. Systematic review and meta‐analyses of papers published in English and Japanese quantified management impacts on species richness and abundance of several taxa, in relation to moderator variables including stand age and management intensity. Plantation thinning substantially increases the richness and abundance of several taxa. Effect sizes decline with time since thinning for the abundance of regenerating saplings and seedlings, necessitating repeated thinning treatments every 6 years to sustain this positive effect. Taxonomic groups exhibit variable relationships with stand age in both planted and secondary forests, indicating a need to include both young and old forest stands in managed forest mosaics. We find an insufficient evidence base is available to allow for a meaningful synthesis of low‐intensity management effects in historically managed secondary forests, with studies varying widely in scale and reported outcomes. We outline an agenda for the research community to achieve a systematic evaluation of scale‐dependent effects of traditional forest management on biodiversity.

The impact of in utero HIV exposure on gut microbiota, inflammation, and microbial translocation

ABSTRACTHIV-exposed but uninfected (HEU) children represent a growing population and show a significantly higher number of infectious diseases, several immune alterations, compromised growth, and increased mortality rates when compared to HIV-unexposed children. Considering the impact that the gut microbiota has on general host homeostasis and immune system development and modulation, we hypothesized that HEU children present altered gut microbiota that is linked to the increased morbidity and the immune system disorders faced by them. Our experiments revealed no differences in beta and alpha diversity of the gut microbiota between HEU and unexposed children or between HIV-infected and uninfected mothers. However, there were differences in the abundance of several taxa from the gut microbiota between HEU and unexposed children and between HIV-infected and uninfected mothers. Functional prediction based on 16S rRNA sequences also indicated differences between HEU and unexposed children and between infected and uninfected mothers. In addition, we detected no differences between HEU and unexposed children in relation to weight, weight-for-age z scores, albumin serum levels, or microbial translocation and inflammation markers. In summary, HIV-infected mothers and their HIV-exposed children present alterations in the abundance of several taxa in the gut microbiome and the predicted functional metagenome when compared to uninfected mothers and unexposed children. Knowledge about the gut microbiome of HEU children in different settings is essential in order to determine better treatments for this susceptible population.

Effect of Lactobacillus reuteri on intestinal microbiota and immune parameters: Involvement of sex differences

Probiotic candidate Lactobacillus reuteri DMSZ 8533 was screened out in vitro based on a relatively higher gastrointestinal tolerance and moderate adhesiveness. The organ index (spleen, thymus and liver), Interleukin-12 (IL-12), tumor necrosis factor-α (TNF-α), T-lymphocytes (CD3-, CD4- and CD-8 positive cells) and fecal microbiota composition were also investigated in BALB/c mice. Results showed a significant higher level of IL-12 at low-dose L. reuteri treated group in both females and males. The relative abundance of phylotypes in the phylum Bacteroidetes and Firmicutes exhibited a reserve shift between sexes after L. reuteri intervention. Meanwhile, the relative abundance of several taxa also differed markedly between sexes at low-dose group, together with microbiota diversity. Our finding demonstrates the importance of L. reuteri DMSZ 8533 as a potential probiotic strain with an immunomodulatory effect, which could also alter the microbiota composition depending on the sex of the host.

Abstract 4076: Gut microbiota and metabolite-driven phenotype modulation in a mouse model of colorectal cancer

Abstract Colorectal cancer (CRC) is a multifactorial disease that develops as a result of multiple genetic mutations, often including loss of the tumor suppressor Adenomatous Polyposis Coli (APC) gene. More recently, additional factors such as the host gut microbiota (GM) have also demonstrated an important role in tumor initiation and progression, yet our understanding of most commensal bacteria remains limited. We observed significant differences in intestinal tumor multiplicity between two ApcMin sub-strain mouse colonies; C57BL/6J-ApcMin (B6-Min/J) mice from The Jackson Laboratory had relatively lower adenoma burden while C57BL/6JD-ApcMin (B6-Min/D) mice from the University of Wisconsin develop twice the number of adenomas. To determine the underlying causes of this phenotypic variability, we used complex microbiota targeted rederivation (CMTR) to rederive embryos of the two Apc mutant sub-strains onto surrogate dams harboring distinct GM from two different vendors (GMJAX and GMHSD), generating four ApcMin groups: B6-Min/JGMJAX, B6-Min/JGMHSD, B6-Min/DGMJAX, and B6-Min/DGMHSD. We observed significant increases in intestinal tumor multiplicity in both B6-Min groups harboring the GMHSD compared to their GMJAX counterparts, suggesting that the GM accounts for a significant portion of variability in tumor phenotype between the ApcMin sub-strains. We characterized the GMJAX and GMHSD microbial populations using 16S rRNA gene sequencing to identify potentially causative and protective bacterial taxa. Relative abundances of several taxa including Bilophila sp., Desulfovibrio sp., and Akkermansia muciniphila, were significantly elevated in GMHSD suggesting pro-tumorigenic roles, while the family Peptococcaceae was more abundant in GMJAX, indicating a potential protective role. To establish the functional output of these distinct GM profiles contributing to tumor development, we used liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to evaluate differences in the intestinal metabolome of the four experimental groups. Notably, we found that the microbiome differences due to colonization with either GMJAX or GMHSD primarily accounted for distinct metabolomic profiles, whereas host genetic differences between the sub-strains had a minimal role in shaping the metabolomes. We detected 31 putative metabolites that were significantly modulated by the GM in both the B6-Min/J and B6-Min/D sub-strains, and were therefore predictive of the relative tumor burden. Moving forward, these metabolites have implications for both biomarker discovery and potential therapeutic and preventative targets. Overall, these results provide insight regarding environmental factors influencing tumorigenesis, and further demonstrate how host-environment interactions can modulate a given disease phenotype. Citation Format: Jacob E. Moskowitz, Zhentian Lei, Susheel Busi, Marcia Hart, Craig Franklin, Lloyd Sumner, James Amos-Landgraf. Gut microbiota and metabolite-driven phenotype modulation in a mouse model of colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4076.

A probiotic modulates the microbiome and immunity in multiple sclerosis.

Effect of a probiotic on the gut microbiome and peripheral immune function in healthy controls and relapsing-remitting multiple sclerosis (MS) patients. MS patients (N = 9) and controls (N = 13) were orally administered a probiotic containing Lactobacillus, Bifidobacterium, and Streptococcus twice-daily for two months. Blood and stool specimens were collected at baseline, after completion of the 2-month treatment, and 3 months after discontinuation of therapy. Frozen peripheral blood mononuclear cells (PBMCs) were used for immune cell profiling. Stool samples were used for 16S rRNA profiling and metabolomics. Probiotic administration increased the abundance of several taxa known to be depleted in MS such as Lactobacillus. We found that probiotic use decreased the abundance of taxa previously associated with dysbiosis in MS, including Akkermansia and Blautia. Predictive metagenomic analysis revealed a decrease in the abundance of several KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways associated with altered gut microbiota function in MS patients, such as methane metabolism, following probiotic supplementation. At the immune level, probiotic administration induced an anti-inflammatory peripheral immune response characterized by decreased frequency of inflammatory monocytes, decreased mean fluorescence intensity (MFI) of CD80 on classical monocytes, as well as decreased human leukocyte antigen (HLA) D related MFI on dendritic cells. Probiotic administration was also associated with decreased expression of MS risk allele HLA-DQA1 in controls. Probiotic-induced increase in abundance of Lactobacillus and Bifidobacterium was associated with decreased expression of MS risk allele HLA.DPB1 in controls. Our results suggest that probiotics could have a synergistic effect with current MS therapies. Ann Neurol 2018.

Bacterial community assembly from cow teat skin to ripened cheeses is influenced by grazing systems

The objectives of this study were to explore bacterial community assembly from cow teat skin to raw milk cheeses and to evaluate the role of farming systems on this assembly using 16S rRNA gene high-throughput sequencing. The two grazing systems studied (extensive vs. semi-extensive) had a greater effect on the microbiota of cow teat skin than on that of raw milks and cheeses. On teat skin, the relative abundance of several taxa at different taxonomic levels (Coriobacteriia, Bifidobacteriales, Corynebacteriales, Lachnospiraceae, Atopobium, and Clostridium) varied depending on the grazing system and the period (early or late summer). In cheese, the abundance of sub-dominant lactic acid bacteria (LAB) varied depending on the grazing system. Overall, 85% of OTUs detected in raw milks and 27% of OTUs detected in ripened cheeses were also found on cow teat skin. Several shared OTUs were assigned to taxa known to be involved in the development of cheese sensory characteristics, such as Micrococcales, Staphylococcaceae, and LAB. Our results highlight the key role of cow teat skin as a reservoir of microbial diversity for raw milk, and for the first time, that cow teat skin serves as a potential source of microorganisms found in raw-milk cheeses.

Anthropogenic water bodies as drought refuge for aquatic macroinvertebrates and macrophytes

Ecological research associated with the importance of refuges has tended to focus on natural rather than anthropogenic water bodies. The frequency of disturbances, including drought events, is predicted to increase in many regions worldwide due to human-induced climate change. More frequent disturbance will affect freshwater ecosystems by altering hydrologic regimes, water chemistry, available habitat and assemblage structure. Under this scenario, many aquatic biota are likely to rely on permanent water bodies as refuge, including anthropogenic water bodies. Here, macroinvertebrate and macrophyte assemblages from waste-water treatment and raw-water storages (i.e. untreated potable water) were compared with nearby natural water bodies during autumn and winter 2013. We expected macroinvertebrate and macrophyte assemblages in raw-water storages to be representative of natural water bodies, while waste-water treatment storages would not, due to degraded water quality. However, water quality in natural water bodies differed from raw-water storages but was similar to waste-water treatment storages. Macroinvertebrate patterns matched those of water quality, with no differences occurring between natural water bodies and waste-water treatment storages, but assemblages in raw-water storages differed from the other two water bodies. Unexpectedly, differences associated with raw-water storages were attributable to low abundances of several taxa. Macrophyte assemblages in raw-water storages were representative of natural water bodies, but were less diverse and abundant in, or absent from, waste-water treatment storages. No clear correlations existed between any habitat variables and macroinvertebrate assemblages but a significant correlation between macrophyte assemblages and habitat characteristics existed. Thus, there were similarities in both water quality and macroinvertebrate assemblages between natural water bodies and waste-water treatment storages, and similarities in macrophyte assemblages between raw-water storages and natural water bodies. These similarities illustrate that anthropogenic water storages support representative populations of some aquatic biota across the landscape, and thus, may provide important refuge following disturbance where dispersal capabilities allow.

Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women

Background: The human milk microbiome has been somewhat characterized, but little is known about changes over time and relations with maternal factors such as nutrient intake.Objective: We sought to characterize the human milk microbiome and described associations with maternal nutrient intake, time postpartum, delivery mode, and body mass index (BMI; in kg/m2).Methods: Milk samples (n = 104) and 24-h diet recalls were collected 9 times from 21 healthy lactating women from day 2 to 6 mo postpartum. Women were classified by BMI as healthy weight (<25) or overweight or obese (≥25). Bacterial taxa were characterized with the use of the high-throughput sequencing of the 16S ribosomal RNA gene.Results: The milk microbiome was relatively constant over time, although there were small changes in some of the lesser-abundant genera. Relative abundances of several taxa were associated with BMI, delivery mode, and infant sex. For instance, overweight and obese mothers produced milk with a higher relative abundance of Granulicatella than did healthy-weight women (1.8% ± 0.6% compared with 0.4% ± 0.2%, respectively; P < 0.05). Relative abundances of several bacterial taxa were also associated with variations in maternal dietary intake. For example, intakes of saturated fatty acids (rs = −0.59; P = 0.005) and monounsaturated fatty acids (rs = −0.46; P = 0.036) were inversely associated with the relative abundance of Corynebacterium; total carbohydrates (rs = −0.54; P = 0.011), disaccharides (rs = −0.47; P = 0.031), and lactose (rs = −0.51; P = 0.018) were negatively associated with Firmicutes; and protein consumption was positively correlated with the relative abundance of Gemella (rs = 0.46; P = 0.037).Conclusions: Factors associated with variations in the human milk microbiome are complex and may include maternal nutrient intake, maternal BMI, delivery mode, and infant sex. Future studies designed to investigate the relation between maternal nutrient intake and the milk microbiome should strive to also evaluate dietary supplement usage and analyze the collected milk for its nutrient content.

Reducing the data-deficiency of threatened European habitats: Spatial variation of sabellariid worm reefs and associated fauna in the Sicily Channel, Mediterranean Sea

Biogenic reefs, such as those produced by tube-dwelling polychaetes of the genus Sabellaria, are valuable marine habitats which are a focus of protection according to European legislation. The achievement of this goal is potentially hindered by the lack of essential empirical data, especially in the Mediterranean Sea. This study addresses some of the current knowledge gaps by quantifying and comparing multi-scale patterns of abundance and distribution of two habitat-forming species (Sabellaria alveolata and S. spinulosa) and their associated fauna along 190 km of coast on the Italian side of the Sicily Channel. While the abundance of the two sabellariids and the total number of associated taxa did not differ at any of the examined scales (from tens of centimetres to tens-100 of kilometres), the structure (composition in terms of both the identity and the relative abundance of constituting taxa) of the associated fauna and the abundance of several taxa (the polychaetes Eulalia ornata, Syllis pulvinata, S. garciai, Nereis splendida and Arabella iricolor, and the amphipods Apolochus neapolitanus, Tethylembos viguieri and Caprella acanthifera) varied among locations established ∼50–100 km apart. Syllis pulvinata also showed significant variation between sites (hundreds of metres apart), analogously to the other syllid polychaetes S. armillaris and S. gracilis, the nereidid polychaete Nereis rava, and the amphipod Gammaropsis ulrici. The largest variance of S. spinulosa, of the structure of the whole associated fauna and of 56% of taxa analysed individually occurred at the scale of replicates (metres apart), while that of the dominant bio-constructor S. alveolata and of 25% of taxa occurred at the scale of sites. The remaining 19% and the total richness of taxa showed the largest variance at the scale of locations. Present findings contribute to meet a crucial requirement of any future effective protection strategy, i.e., identifying relevant scales of variation to be included in protection schemes aiming at preserving representative samples not only of target habitats and organisms, but also of the processes driving such variability.

Reefcrete: Reducing the environmental footprint of concretes for eco-engineering marine structures

The ecological value of engineered marine structures can be enhanced by building-in additional habitat complexity. Pre-fabricated habitat units can be cheaply and easily cast from concrete into heterogeneous three-dimensional shapes and surface topographies, with proven ability to enhance biodiversity on artificial structures. The net ecological benefits of enhancement using concrete, however, may be compromised on account of its large environmental footprint and poor performance as substrate for many marine organisms. We carried out a pilot study to trial alternative cast-able “Reefcrete” concrete mixes, with reduced environmental footprints, for use in the marine environment. We used partial replacement of Portland cement with recycled ground granulated blast-furnace slag (GGBS), and partial replacement of coarse aggregate with hemp fibres and recycled shell material. We calculated the estimated carbon footprint of each concrete blend and deployed replicate tiles in the intertidal environment for 12 months to assess their performance as substrate for marine biodiversity. The hemp and shell concrete blends had reduced carbon footprints compared to both ordinary Portland cement based concrete and the GGBS based control concrete used in this study. At the end of the experiment, the hemp and shell blends supported significantly more live cover than the standard GGBS control blend. Taxon richness, particularly of mobile fauna, was also higher on the hemp concrete than either the shell or GGBS control. Furthermore, the overall species pool recorded on the hemp concrete was much larger. Community compositions differed significantly on the hemp tiles, compared to GGBS controls. This was largely explained by higher abundances of several taxa, including canopy-forming algae, which may have facilitated other taxa. Our findings indicate that the alternative materials trialled in this study provided substrate of equal or better habitat suitability compared to ordinary GGBS based concrete. Given the growing interest in ecological engineering of marine infrastructure, we propose there would be great benefit in further development of these alternative “Reefcrete” materials for wider application.

Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome.

There is mounting evidence for a connection between the gut and Parkinson's disease (PD). Dysbiosis of gut microbiota could explain several features of PD. The objective of this study was to determine if PD involves dysbiosis of gut microbiome, disentangle effects of confounders, and identify candidate taxa and functional pathways to guide research. A total of 197 PD cases and 130 controls were studied. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from stool. Metadata were collected on 39 potential confounders including medications, diet, gastrointestinal symptoms, and demographics. Statistical analyses were conducted while controlling for potential confounders and correcting for multiple testing. We tested differences in the overall microbial composition, taxa abundance, and functional pathways. Independent microbial signatures were detected for PD (P = 4E-5), participants' region of residence within the United States (P = 3E-3), age (P = 0.03), sex (P = 1E-3), and dietary fruits/vegetables (P = 0.01). Among patients, independent signals were detected for catechol-O-methyltransferase-inhibitors (P = 4E-4), anticholinergics (P = 5E-3), and possibly carbidopa/levodopa (P = 0.05). We found significantly altered abundances of the Bifidobacteriaceae, Christensenellaceae, [Tissierellaceae], Lachnospiraceae, Lactobacillaceae, Pasteurellaceae, and Verrucomicrobiaceae families. Functional predictions revealed changes in numerous pathways, including the metabolism of plant-derived compounds and xenobiotics degradation. PD is accompanied by dysbiosis of gut microbiome. Results coalesce divergent findings of prior studies, reveal altered abundance of several taxa, nominate functional pathways, and demonstrate independent effects of PD medications on the microbiome. The findings provide new leads and testable hypotheses on the pathophysiology and treatment of PD. © 2017 International Parkinson and Movement Disorder Society.

Seasonal Succession of Free-Living Bacterial Communities in Coastal Waters of the Western Antarctic Peninsula.

The marine ecosystem along the Western Antarctic Peninsula undergoes a dramatic seasonal transition every spring, from almost total darkness to almost continuous sunlight, resulting in a cascade of environmental changes, including phytoplankton blooms that support a highly productive food web. Despite having important implications for the movement of energy and materials through this ecosystem, little is known about how these changes impact bacterial succession in this region. Using 16S rRNA gene amplicon sequencing, we measured changes in free-living bacterial community composition and richness during a 9-month period that spanned winter to the end of summer. Chlorophyll a concentrations were relatively low until summer when a major phytoplankton bloom occurred, followed 3 weeks later by a high peak in bacterial production. Richness in bacterial communities varied between ~1,200 and 1,800 observed operational taxonomic units (OTUs) before the major phytoplankton bloom (out of ~43,000 sequences per sample). During peak bacterial production, OTU richness decreased to ~700 OTUs. The significant decrease in OTU richness only lasted a few weeks, after which time OTU richness increased again as bacterial production declined toward pre-bloom levels. OTU richness was negatively correlated with bacterial production and chlorophyll a concentrations. Unlike the temporal pattern in OTU richness, community composition changed from winter to spring, prior to onset of the summer phytoplankton bloom. Community composition continued to change during the phytoplankton bloom, with increased relative abundance of several taxa associated with phytoplankton blooms, particularly Polaribacter. Bacterial community composition began to revert toward pre-bloom conditions as bacterial production declined. Overall, our findings clearly demonstrate the temporal relationship between phytoplankton blooms and seasonal succession in bacterial growth and community composition. Our study highlights the importance of high-resolution time series sampling, especially during the relatively under-sampled Antarctic winter and spring, which enabled us to discover seasonal changes in bacterial community composition that preceded the summertime phytoplankton bloom.