Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature

The Bacteroidetes phylum is renowned for its ability to degrade a wide range of complex carbohydrates, a trait that has enabled its dominance in many diverse environments. The best studied species inhabit the human gut microbiome and use polysaccharide utilization loci (PULs), discrete genetic structures that encode proteins involved in the sensing, binding, deconstruction, and import of target glycans. In many environmental species, polysaccharide degradation is tightly coupled to the phylum-exclusive type IX secretion system (T9SS), which is used for the secretion of certain enzymes and is linked to gliding motility. In addition, within specific species these two adaptive systems (PULs and T9SS) are intertwined, with PUL-encoded enzymes being secreted by the T9SS. Here, we discuss the most noteworthy PUL and non-PUL mechanisms that confer specific and rapid polysaccharide degradation capabilities to the Bacteroidetes in a range of environments. We also acknowledge that the literature showcasing examples of PULs is rapidly expanding and developing a set of assumptions that can be hard to track back to original findings. Therefore, we present a simple universal description of conserved PUL functions and how they are determined, while proposing a common nomenclature describing PULs and their components, to simplify discussion and understanding of PUL systems

Dietary replacement of fishmeal with marine proteins recovered from shrimp and herring process waters promising in Atlantic salmon aquaculture

There is a general agreement that fish meal (FM) and fish oil (FO) are valuable resources for aquafeed, but that the production cannot keep the same pace as the current growth of the aquaculture industry. Therefore, there is a need to find alternative sources for lipids and protein. This study examines the possibility of using proteins recovered from seafood industry side stream waters as a complement to FM in feed for Atlantic salmon. To recover the proteins, herring and shrimp process side streams waters were flocculated then treated with dissolved air flotation (DAF), which is considered a gentle technology. Shrimp steam water was used to obtain shrimp protein (SP) and herring salt brine to obtain herring protein (HP). The recovered semi-solid protein fraction was spray dried and formulated into experimental diets at inclusion levels of 1.9–10% (dw/dw). Two feeding trials were conducted to investigate; 1) the properties of different flocculants to recover SP from shrimp steam water, alginate (Alg; 1.9% inclusion), carrageenan (Carr; 2.0% inclusion) and a synthetic flocculant from Kemira (Kem; 3.8% inclusion). 2) total or partial replacement of FM with SP-Alg (10% and no FM) and HP-Alg (3% and 8% FM). For both feeding trials each diet was provided to triplicate tanks (n = 31 and 30/tank) of Atlantic salmon with a start weight of 193 g (duration 10 weeks) and 304 g (duration 7 weeks) respectively. All fish showed similar feed intake, feed conversion ratio (on tank basis) and weight gain. The inclusion of SP or HP as total or partial replacement of FM did neither influence adiposity of the fish, as measured by condition factor, nor heposomatic index (HSI). No negative effect of the alternative protein could be found through histological examination of the intestine. In feeding trial two, diets did not affect the adaptive immune indicators CD8α and MHC II. The SP-Alg diet did not affect intestinal barrier and transporting functions, assessed using Ussing-chamber technology. However, HP-Alg affected the trans-epithelial resistance, which indicate that the intestinal barrier function could be affected by low inclusions. We conclude that from a biological perspective, SP recovered from shrimp steaming waters using Alg and DAF technology represents a new marine biomass with potential as a replacement for FM in Atlantic salmon feed. To diversify the possibility of using flocculants to retrieve proteins we also suggest further investigation of the potential to use Carr in larger inclusions

Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut

Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. Here, we test the accuracy of AcGGM within the complex endogenous gut microbiome of pigs, wherein we resolve 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially express AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifests a “butterfly effect”, whereby numerous metabolic changes and interdependent cross-feeding pathways occur in neighboring non-mannanolytic populations that produce short-chain fatty acids. Our findings show how intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large