The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission.

Bacteriophages are influential within the human gut microbiota, yet they remain understudied relative to bacteria. This is a limitation of studies on fecal microbiota transplantation (FMT) where bacteriophages likely influence outcome. Here, using metagenomics, we profile phage populations - the phageome - in individuals recruited into two double-blind randomized trials of FMT in ulcerative colitis.

Bacterial and Symbiodiniaceae communities' variation in corals with distinct traits and geographical distribution.

Coral microbiomes play crucial roles in holobiont homeostasis and adaptation. The host's ability to populate broad ecological niches and to cope with environmental changes seems to be related to the flexibility of the coral microbiome. By means of high-throughput DNA sequencing we characterized simultaneously both bacterial (16S rRNA) and Symbiodiniaceae (ITS2) communities of four reef-building coral species (Mussismilia braziliensis, Mussismilia harttii, Montastraea cavernosa, and Favia gravida) that differ in geographic distribution and niche specificity.

Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont.

Holobionts are highly organized assemblages of eukaryotic hosts, cellular microbial symbionts, and viruses, whose interactions and evolution involve complex biological processes. It is largely unknown which specific determinants drive similarity or individuality in genetic diversity between holobionts. Here, we combine short- and long-read sequencing and DNA-proximity-linkage technologies to investigate intraspecific diversity of the microbiomes, including host-resolved viruses, in individuals of a model marine sponge.

The Effect of Face Mask Wear on the Ocular Surface and Contact Lens Microbiome.

Objectives: As face mask wear can result in the redirection of nasal and oral exhalation toward the ocular region, this study investigated the impact of face mask wear on the conjunctiva, eyelid margin, and contact lens (CL) surface microbiome.

Methods: In this prospective, cross-over study, experienced CL wearers (N=20) were randomized to wear a face mask for 6 hr/day (minimum) for a week or no mask for a week. The conjunctiva, eyelid, and CLs were then sampled.

Refining microbial community metabolic models derived from metagenomics using reference-based taxonomic profiling.

Characterization of microbial community metabolic output is crucial to understanding their functions. Construction of genome-scale metabolic models from metagenome-assembled genomes (MAG) has enabled prediction of metabolite production by microbial communities, yet little is known about their accuracy. Here, we examined the performance of two approaches for metabolite prediction from metagenomes, one that is MAG-guided and another that is taxonomic reference-guided.

Non-selective microbiota reduction after the elicitation of a seaweed's immune response.

Pattern-triggered immunity (PTI) is an integral part of the innate immune system of many eukaryotic hosts, assisting in the defence against pathogen invasions. In plants and animals, PTI exerts a selective pressure on the microbiota that can alter community composition. However, the effect of PTI on the microbiota for non-model hosts, including seaweeds, remains unknown.

Not all parents are the same: Diverse strategies of symbiont transmission in seaweeds.

Different marine seaweed species have been shown to harbour specific bacterial communities, however, the extent to which vertical symbiont transmission from parents to offspring contributes to host-specificity is unclear. Here we use fluorescence and electron microscopy as well as 16S rRNA gene-based community analysis to investigate symbiont transmission in members of the three major seaweed groups (green Chlorophyta, red Rhodophyta and brown Phaeophyceae). We found seaweeds employ diverse strategies to transfer symbionts to their progeny.

The impact of interspecific competition on the genomic evolution of Phaeobacter inhibens and Pseudoalteromonas tunicata during biofilm growth.

Interspecific interactions in biofilms have been shown to cause the emergence of community-level properties. To understand the impact of interspecific competition on evolution, we deep-sequenced the dispersal population of mono- and co-culture biofilms of two antagonistic marine bacteria (Phaeobacter inhibens 2.10 and Pseudoalteromononas tunicata D2).

Ocular microbiome changes in dry eye disease and meibomian gland dysfunction.

The most common and chronic ocular problem of aging is dry eye disease (DED) and the associated condition of meibomian gland dysfunction (MGD). The resident ocular surface bacteria may have a role in maintaining homeostasis and perturbation may contribute to disease development. The aim of this study was to compare the microbiomes of the conjunctiva and eyelid margin in humans with mild and moderate DED and controls using 16 S rRNA gene sequencing.

Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae.

Sponges thrive in the deep, dark and nutrient-depleted ocean and may rely on microbial symbionts for carbon acquisition and energy generation. However, these symbiotic relationships remain largely unexplored. In this study, we analyze the microbiome of deep-sea sponges and show that ammonia-oxidizing archaea (AOA) of the family Nitrosopumilaceae make up at least 75% of the microbial communities of the sponges Aphrocallistes sp.

The Algal Polysaccharide Ulvan and Carotenoid Astaxanthin Both Positively Modulate Gut Microbiota in Mice.

The intestinal microbial community (microbiota) is dynamic and variable amongst individuals and plays an essential part in gut health and homeostasis. Dietary components can modulate the structure of the gut microbiota. In recent years, substantial efforts have been made to find novel dietary components with positive effects on the gut microbial community structure.

Differential priority effects impact taxonomy and functionality of host-associated microbiomes.

Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown.

as a Microalgal Food Intervention in Diet-Induced Metabolic Syndrome in Rats.

The microalgal genus has broad applicability to produce biofuels, animal feed supplements and other value-added products including proteins, carotenoids and lipids. This study investigated a potential role of in the reversal of metabolic syndrome. Male Wistar rats ( = 48) were divided into four groups in a 16-week protocol.

Coffee Pulp, a By-Product of Coffee Production, Modulates Gut Microbiota and Improves Metabolic Syndrome in High-Carbohydrate, High-Fat Diet-Fed Rats.

Waste from food production can be re-purposed as raw material for usable products to decrease industrial waste. Coffee pulp is 29% of the dry weight of coffee cherries and contains caffeine, chlorogenic acid, trigonelline, diterpenes and fibre. We investigated the attenuation of signs of metabolic syndrome induced by high-carbohydrate, high-fat diet in rats by dietary supplementation with 5% freeze-dried coffee pulp for the final 8 weeks of a 16-week protocol.

Cross-Host Protection of Marine Bacteria Against Macroalgal Disease.

Despite an increasing awareness of disease impacts on both cultivated and native seaweed populations, the development of marine probiotics has been limited and predominately focused on farmed animals. Bleaching (loss of thallus pigmentation) is one of the most prevalent diseases observed in marine macroalgae. Endemic probiotic bacteria have been characterized to prevent bleaching disease in red macroalgae Agarophyton vermiculophyllum and Delisea pulchra; however, the extent to which probiotic strains provide cross-protection to non-endemic hosts and the influence of native microbiota remain unknown.

Bacterial controlled mitigation of dysbiosis in a seaweed disease.

Disease in the marine environment is predicted to increase with anthropogenic stressors and already affects major habitat-formers, such as corals and seaweeds. Solutions to address this issue are urgently needed. The seaweed Delisea pulchra is prone to a bleaching disease, which is caused by opportunistic pathogens and involves bacterial dysbiosis.

Genomic Evolution of the Marine Bacterium Phaeobacter inhibens during Biofilm Growth.

Phaeobacter inhibens 2.10 is an effective biofilm former on marine surfaces and has the ability to outcompete other microorganisms, possibly due to the production of the plasmid-encoded secondary metabolite tropodithietic acid (TDA). P.

Stress response of the marine sponge Scopalina sp.. Can microbial community composition predict sponge disease?

Disease has become an increasingly recognised problem in the marine environment, but our understanding of the factors that drive disease or our ability to predict its occurrence is limited. Marine sponges are known for their close associations with microorganisms, which are generally accepted to underpin sponge health and function. The aim of this study is to explore whether the microbial community composition of sponges can act as a predictor of disease occurrence under stressful environmental conditions.

Brown Seaweed as an Intervention for Diet-Induced Obesity in Male Wistar Rats.

The therapeutic potential of grown in Australian tropical waters was tested in a rat model of metabolic syndrome. Forty-eight male Wistar rats were divided into four groups of 12 rats and each group was fed a different diet for 16 weeks: corn starch diet (C); high-carbohydrate, high-fat diet (H) containing fructose, sucrose, saturated and fats; and C or H diets with 5% mixed into the food from weeks 9 to 16 (CS and HS). Obesity, hypertension, dyslipidaemia, impaired glucose tolerance, fatty liver and left ventricular fibrosis developed in H rats.

Comparative analysis of ocular surface tissue microbiome in human, mouse, rabbit, and guinea pig.

Animal models are a critical element of ocular surface research for investigating therapeutic drops, surgical implants, and infection research. This study was a comparative analysis of the microbial communities on conjunctival tissue samples from humans compared to several commonly used laboratory animals (BALB/c mice, New Zealand white rabbits and IMVS colored stock guinea pigs). Microbial communities were analyzed by extracting total DNA from conjunctival tissue and sequencing the 16 S rRNA gene using the Illumina MiSeq platform.

Combating Parasitic Nematode Infections, Newly Discovered Antinematode Compounds from Marine Epiphytic Bacteria.

Parasitic nematode infections cause debilitating diseases and impede economic productivity. Antinematode chemotherapies are fundamental to modern medicine and are also important for industries including agriculture, aquaculture and animal health. However, the lack of suitable treatments for some diseases and the rise of nematode resistance to many available therapies necessitates the discovery and development of new drugs.

(Sea Grapes) Improves Cardiovascular and Metabolic Health of Rats with Diet-Induced Metabolic Syndrome.

(sea grapes) is widely consumed in South-East Asia as a low-energy food with high contents of vitamins and minerals. This study investigated dried sea grapes containing 16.6% insoluble fibre commercially produced in Vietnam as an intervention.

Carrageenans from the Red Seaweed Attenuate Symptoms of Diet-Induced Metabolic Syndrome in Rats.

Carrageenans are thickening and gelling agents that may provide health benefits. Iota (ι)-carrageenan, a linear sulfated polysaccharide, is produced by the red seaweed, . This study investigated the potential of this seaweed as a functional food for the reversal of metabolic syndrome and possible mechanisms.

Physiological and Metabolic Effects of Yellow Mangosteen () Rind in Rats with Diet-Induced Metabolic Syndrome.

Metabolic syndrome is a cluster of disorders that increase the risk of cardiovascular disease and diabetes. This study has investigated the responses to rind of yellow mangosteen (), usually discarded as waste, in a rat model of human metabolic syndrome. The rind contains higher concentrations of phytochemicals (such as garcinol, morelloflavone and citric acid) than the pulp.

Phaeobacter inhibens controls bacterial community assembly on a marine diatom.

Bacterial communities can have an important influence on the function of their eukaryotic hosts. However, how microbiomes are formed and the influence that specific bacteria have in shaping these communities is not well understood. Here, we used the marine diatom Thalassiosira rotula and the algal associated bacterium Phaeobacter inhibens as a model system to explore these questions.