Prebiotics are increasingly examined for their ability to modulate the neonate gut microbiota of livestock and products such as inulin are commonly added to milk replacer used in calving. However, the ability of specific members of the bovine neonate microbiota to respond to inulin remains to be determined, particularly among indigenous lactobacilli and bifidobacteria, beneficial genera commonly enriched by inulin. Screening of Bifidobacterium and Lactobacillus isolates obtained from fresh feces of dairy calves revealed that lactobacilli had a higher prevalence of inulin fermentation capacity (58%) than bifidobacteria (17%). Several Ligilactobacillus agilis comb. nov. (formerly Lactobacillus agilis) isolates exhibited vigorous growth on, and complete degradation of, inulin however the phenotype was strain-specific. The most vigorous inulin fermenting strain, L. agilis YZ050, readily degraded long chain inulin not consumed by bifidobacterial isolates. Comparative genomic analysis of both L. agilis fermenter and non-fermenter strains indicated that strain YZ050 encodes an inulinase homolog, previously linked to extracellular degradation of long-chain inulin in Lacticaseibacillus paracasei comb. nov., that was strongly induced during growth on inulin. Inulin catabolism by YZ050 also generates extracellular fructose which can serve as a growth substrate to cross feed other non-inulin-fermenting lactic acid bacteria isolated from the same bovine feces. The presence of specific inulin-responsive bacterial strains within calf gut microbiome provides a mechanistic rationale for enrichment of specific lactobacilli and creates a foundation for future synbiotic applications in dairy calves aimed at improving health in early life. IMPORTANCE The gut microbiome plays an important role in animal health and is increasingly recognized as a target for diet-based manipulation. Inulin is a common prebiotic routinely added to animal feeds, however, the mechanism of inulin consumption by specific beneficial taxa in livestock is ill defined. In this study we examined Lactobacillus and Bifidobacterium isolates from calves fed inulin-containing milk replacer and characterized specific strains that robustly consume long chain inulin. In particular, a novel Ligilactobacillus agilis strain YZ050 consumed inulin via an extracellular fructosidase resulting in complete consumption of all long chain inulin. Inulin catabolism resulted in temporal release of extracellular fructose that can promote growth of other non-inulin consuming LAB strains. This work provides the mechanistic insight needed to purposely modulate the calf gut microbiome via the establishment of networks of beneficial microbes linked to specific prebiotics.

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BACKGROUND Cassava leaves are an abundant global agricultural residue because the roots are a major source of dietary carbohydrates. Although cassava leaves are high in protein, the protein is not bioavailable. This work aimed to convert cassava leaves to a bioavailable protein‐rich animal feed ingredient using high‐protein yeasts. RESULTS The structural proteins (ca 200 g kg−1 d.b.) from sundried cassava leaves were solubilized by mild alkali pretreatment, and the resulting cassava leaf hydrolysate (CLH) was used to screen for growth of 46 high‐protein yeasts from 30 species. Promising candidates from the initial screen cultivated at a 10 mL scale demonstrated increases in relative abundance of essential amino acids over that of CLH. In particular, lysine, growth‐limiting for some livestock, was increased up to 226% over the CLH content. One yeast, Pichia kudriavzevii UCDFST 11‐602, was grown in 3 L of CLH in a bioreactor to examine the scale‐up potential of the yeast protein production. While glucose was completely consumed, yeast growth exited log phase before depleting either carbon or nitrogen, suggesting other growth‐limiting factors at the larger scale. CONCLUSIONS High‐value animal feed with enriched essential amino acid profiles can be produced by yeasts grown on agricultural residues. Yeasts convert structural protein solubilized from cassava leaves to essential amino acid‐enriched, digestible protein. The low carbohydrate content of the leaves (ca 200 g kg−1 d.b.), however, necessitated glucose supplementation for yeast growth. © 2018 Society of Chemical Industry

The olive fruit fly (Bactrocera oleae Rossi) is the primary insect pest in all olive-growing regions worldwide. New integrated pest management (IPM) techniques are needed for B. oleae to mitigate reliance on pesticides used for its control which can result in negative environmental impacts. More effective lures for monitoring olive flies would help to know when and where direct chemical applications are required. The aim of this research was to find new, more effective methods for B. oleae detection and monitoring. Twelve insect-associated yeasts were selected and tested as living cultures in McPhail traps for the attraction of olive flies. Certain yeasts were more attractive than others to B. oleae; specifically, Kuraishia capsulata, Lachancea thermotolerans, Peterozyma xylosa, Scheffersomyces ergatensis, and Nakazawae ernobii, than the industry-standard dried torula yeast (Cyberlindnera jadinii; syn. Candida utilis). The attractiveness of dry, inactive (i.e., non-living) formulations of these five yeasts was also tested in the field. Inactive formulations of K. capsulata, P. xylosa, N. ernobii, and L. thermotolerans were significantly more attractive to B. oleae than commercially available torula yeast. Green lacewing, Chrysoperla comanche (Stephens) (Neuroptera: Chrysopidae), adults were incidentally caught in traps baited with the live yeast cultures. This is the first field study that compares olive fly attraction to yeast species other than torula yeast. Commercialization of yeasts that are more attractive than the torula standard would improve monitoring and associated control of the olive fruit fly.

Pretreatment with ionic liquids (IL) such as 1-ethyl-3-methylimidazolium chloride or acetate is an effective method for aiding deconstruction of lignocellulosic biomass; however, the residual IL remaining in hydrolysates can be inhibitory to growth of ethanologenic or oleaginous yeasts that have been examined in the literature. The aim of this study was to identify oleaginous yeasts that are tolerant of the IL [CCIm][OAc] and [CCIm]Cl using 45 strains belonging to 38 taxonomically diverse species within phyla Ascomycota and Basidiomycota. Yeasts were cultivated in laboratory medium supplemented with 0, 2, or 4% IL in 96-well plates. The eight most tolerant strains were then cultivated in 10-mL media with no IL, 242mM [CCIm][OAc], or 242mM [CCIm]Cl. The effects of [CCIm] exposure on cell mass production and lipid accumulation varied at the species and strain level. The acetate salt decreased cell biomass and lipid production more severely than did the chloride ion for six strains. Lipid output was not markedly different (2.1 vs. 2.3 g/L) in Yarrowia lipolytica UCDFST 51-30, but decreased from 5 to 65% in other yeasts. An equimolar concentration of the chloride salt resulted in much milder effects, from 25% decrease to 66% increase in lipid output. The highest lipid outputs in this media were 8.3 and 7.9 g/L produced by Vanrija humicola UCDFST 10-1004 and UCDFST 12-717, respectively. These results demonstrated substantial lipid production in the presence of [CCIm]Cl at concentrations found in lignocellulosic hydrolysates, and thus, these two strains are ideal candidates for further investigation.