Exploring rumen microbe-derived fibre-degrading activities for improving feed digestibility

Ruminal fibre degradation is mediated by a complex community of rumen microbes, and its efficiency is crucial for optimal dairy productivity. Enzymes produced by rumen microbes are primarily responsible for degrading the complex structural polysaccharides that comprise fibre in the plant cell walls of feed materials. Because rumen microbes have evolved with their ruminant hosts over millions of years to perform this task, their enzymes are hypothesised to be optimally suited for activity at the temperature, pH range, and anaerobic environment of the rumen. However, fibre-rich diets are not fully digested, which represents a loss in potential animal productivity. Thus, there is opportunity to improve fibre utilisation through treating feeds with rumen microbe-derived fibrolytic enzymes and associated activities that enhance fibre degradation. This research aims to gain a better understanding of the key rumen microbes involved in fibre degradation and the mechanisms they employ to degrade fibre, by applying cultivation-based and culture-independent genomics approaches to rumen microbial communities of New Zealand dairy cattle. Using this knowledge, we aim to identify new opportunities for improving fibre degradation to enhance dairy productivity. Rumen content samples were taken over the course of a year from a Waikato dairy production herd. Over 1,000 rumen bacterial cultures were obtained from the plant-adherent fraction of the rumen contents. Among these cultures, two, 59 and 103 potentially new families, genera and species of rumen bacteria were identified, respectively. Many of the novel strains are being genome sequenced within the Hungate 1000 rumen microbial reference genome programme, which is providing deeper insights into the range of mechanisms used by the individual strains for fibre degradation. This information has been used to guide the selection of rumen bacterial strains with considerable potential as fibrolytic enzyme producers in vitro, with the intent of developing the strains so that their enzymes may be used as feed pre-treatments for use on farm. Culture-independent metagenomic approaches were also used to explore the activities involved in fibre degradation from the rumen microbial communities. Functional screening has revealed a range of novel enzymes and a novel fibre disrupting activity. Enrichment for the cell-secreted proteins from the community revealed evidence of a diverse range of cellulosomes, which are cell-surface associated multi-enzyme complexes that efficiently degrade plant cell wall polysaccharides. Biochemical and structural characterisation of these proteins has been conducted. In conclusion, cultivation and culture-independent genomic approaches have been applied to New Zealand bovine rumen microbial communities, and have provided considerable new insights into ruminal fibre degradation processes. Novel activities and bacterial species that display desirable activities on fibrous substrates in vitro are now being explored for their potential to improve ruminal fibre degradation, to allow the development of new technologies that will enhance dairy productivity

Überblick über Spurenelemente in Böden der Aue der Mittleren Elbe

Floodplain soils across the Central Elbe River, Germany, have unique features. These soils vary considerably in their properties due to rapid fluvial processes and in metal contents due to frequent industrial discharge into the river. Although there have been works studying such soils, there has never been a comprehensive study that would monitor a large number of entire soil profiles along the Elbe River. Our aim was to describe the main properties of 94 profiles representing different soils along the Elbe River, their content from 15 potentially toxic elements (PTEs) in various depths, and assess various soil contamination and health risk indices. We measured soil properties auch as pH, organic carbon (OC), particle size distribution, as well as total concentrations of aluminium (Al), arsenic (As), barium (Ba), chromium (Cr), copper (Cu), iron (Fe), manganese (Mn), lead (Pb), nickel (Ni), rubidium (Rb), strontium (Sr), tin (Sn), vanadium (V), zirconium (Zr), and zinc (Zn) in all soil profiles. We presented the data for all soil horizons and in top- (0-30 cm depth) and subsoil (>30 cm depth). We found that pH, OC, and clay differed significantly between top- and subsoil horizons reflecting different water regimes and other factors. On the other hand, Al, Fe, and Mn were not affected significantly by depth. Among the studied PTEs, Sn was found to be generating the highest values in Contamination Factor, Geoaccumulation Index, and Enrichment Factor; it was followed by As, Zn, and Pb. Other PTEs such as Ba, Rb, Sr, V, and Zr, and exhibited much lower soil contamination index values. The Pollution Load Index was very high. Health risk assessment indicated rather unexpectedly that Zr was the primary contributor to total risk. We conclude that in multi-element contamination cases, even PTEs with low soil concentrations (such as Zr here) may have predominant role in the risk related to soil contamination

Phylogenetic Evidence for Lateral Gene Transfer in the Intestine of Marine Iguanas

Background: Lateral gene transfer (LGT) appears to promote genotypic and phenotypic variation in microbial communities in a range of environments, including the mammalian intestine. However, the extent and mechanisms of LGT in intestinal microbial communities of non-mammalian hosts remains poorly understood. Methodology/Principal Findings: We sequenced two fosmid inserts obtained from a genomic DNA library derived from an agar-degrading enrichment culture of marine iguana fecal material. The inserts harbored 16S rRNA genes that place the organism from which they originated within Clostridium cluster IV, a well documented group that habitats the mammalian intestinal tract. However, sequence analysis indicates that 52 % of the protein-coding genes on the fosmids have top BLASTX hits to bacterial species that are not members of Clostridium cluster IV, and phylogenetic analysis suggests that at least 10 of 44 coding genes on the fosmids may have been transferred from Clostridium cluster XIVa to cluster IV. The fosmids encoded four transposase-encoding genes and an integrase-encoding gene, suggesting their involvement in LGT. In addition, several coding genes likely involved in sugar transport were probably acquired through LGT. Conclusion: Our phylogenetic evidence suggests that LGT may be common among phylogenetically distinct members o

Genome-scale analyses of health-promoting bacteria: probiogenomics

The human body is colonized by an enormous population of bacteria (microbiota) that provides the host with coding capacity and metabolic activities. Among the human gut microbiota are health-promoting indigenous species (probiotic bacteria) that are commonly consumed as live dietary supplements. Recent genomics-based studies (probiogenomics) are starting to provide insights into how probiotic bacteria sense and adapt to the gastrointestinal tract environment. In this Review, we discuss the application of probiogenomics in the elucidation of the molecular basis of probiosis using the well-recognized model probiotic bacteria genera Bifidobacterium and Lactobacillus as examples

Lithostratigraphy of the Palaeoproterozoic Hekpoort formation (Pretoria Group, Transvaal Supergroup), South Africa

The Palaeoproterozoic Hekpoort Formation of the Pretoria Group is a lava-dominated unit that has a basin-wide extent throughout the Transvaal sub-basin of South Africa. Additional correlative units may be present in the Kanye sub-basin of Botswana. The key characteristic of the formation is its general geochemical uniformity. Volcaniclastic and other sedimentary rocks are relatively rare throughout the succession but may be dominant in some locations. Hekpoort Formation outcrops are sporadic throughout the basin and mostly occur in the form of gentle hills and valleys, mainly encircling Archaean domes and the Palaeoproterozoic Bushveld Complex (BC). The unit is exposed in the western Pretoria Group basin, sitting unconformably either on the Timeball Hill Formation or Boshoek Formation, which is lenticular there, and on top of the Boshoek Formation in the east of the basin. The unit is unconformably overlain by the Dwaalheuwel Formation. The type-locality for the Hekpoort Formation is the Hekpoort farm (504 IQ Hekpoort), ca. 60 km to the west-southwest of Pretoria. However, no stratotype has ever been proposed. A lectostratotype, i.e., the Mooikloof area in Pretoria East, that can be enhanced by two reference stratotypes are proposed herein. The Hekpoort Formation was deposited in a cratonic subaerial setting, forming a large igneous province (LIP) in which short-termed localised ponds and small braided river systems existed. It therefore forms one of the major Palaeoproterozoic magmatic events on the Kaapvaal Craton.http://sajg.geoscienceworld.orgam2021Geolog

Pore and Grain Geometry Analysis of Sandstone Reservoir Rocks from a Well of a Northern German Basin

Pore space and grain geometry are important physical properties distinguished in reservoir rocks, particularly in sandstones, due to their influence on oil and gas reservoir quality. Therefore, a detailed study of pore space morphology and grain surface roughness in sandstone reservoir rocks is a key element in petroleum geology. It is eminent in understanding of the adhesion of hydrocarbons in rocks and coupled fluid flows in pores and along grain surfaces. In this work, sandstone samples taken from a well of a Northern German basin deposit have been analysed by thin section petrography, Confocal Raman Microscopy and Confocal Laser Scanning Microscopy (CLSM). The roughness of grain surfaces is analysed and the pore geometries of sandstone rocks are verified. Roughness and pore geometry have a significant impact on the wetting behaviour and adhesion properties of hydrocarbon fluids, water or carbon dioxide (CO2) to the pore walls. The results show the relationship between the composition of sandstones and their pore geometry and the grain surface roughness. The geometry of the pore morphology and the grain surface shows a range from very rough to flat smooth crystal facets, from few hundreds to sub-micron, depending on the scale of observation. The 50x and 100x magnifications were applied in this study. The findings offer a detailed insight into the relationship of pore space morphology and the grain surface roughness. The results add important parameters to the calculation models for hydrocarbon exploitation and to enhancement of the amount of oil recovery

"Nourish to Flourish": complementary feeding for a healthy infant gut microbiome-a non-randomised pilot feasibility study.

BACKGROUND: The introduction of complementary foods and changes in milk feeding result in modifications to gastrointestinal function. The interplay between indigestible carbohydrates, host physiology, and microbiome, and immune system development are areas of intense research relevant to early and later-life health. METHODS: This 6-month prospective non-randomised feasibility study was conducted in Auckland, New Zealand (NZ), in January 2018. Forty parents/caregivers and their infants were enrolled, with 30 infants allocated to receive a prebiotic NZ kūmara (flesh and skin; a type of sweet potato) prepared as a freeze-dried powder, and ten infants allocated to receive a commercially available probiotic control known to show relevant immune benefits (109 CFU Bifidobacterium lactis BB-12®). The primary outcome was the study feasibility measures which are reported here. RESULTS: Recruitment, participant retention, and data collection met feasibility targets. Some limitations to biological sample collection were encountered, with difficulties in obtaining sufficient plasma sample volumes for the proposed immune parameter analyses. Acceptability of the kūmara powder was met with no reported adverse events. CONCLUSION: This study indicates that recruiting infants before introducing complementary foods is feasible, with acceptable adherence to the food-based intervention. These results will inform the protocol of a full-scale randomised controlled trial (RCT) with adjustments to the collection of biological samples to examine the effect of a prebiotic food on the prevalence of respiratory tract infections during infancy. Trial registration Australia New Zealand Clinical Trials Registry ACTRN12618000157279 . Prospectively registered on 02/01/2018.fals

Extensive bacteriocin gene shuffling in the Streptococcus bovis/Streptococcus equinus complex reveals gallocin D with activity against vancomycin resistant enterococci

peer-reviewedStreptococcus gallolyticus LL009 produces gallocin D, a narrow spectrum two component bacteriocin with potent activity against vancomycin-resistant enterococci. Gallocin D is distinct from gallocin A, a separate two component bacteriocin produced by S. gallolyticus. Although the gene clusters encoding gallocin A and gallocin D have a high degree of gene synteny, the structural genes are highly variable and appear to have undergone gene shufing with other streptococcal species. Gallocin D was analysed in laboratory-based experiments. The mature peptides are 3,343± 1 Da and 3,019 ± 1 Da and could be readily synthesized and display activity against a vancomycin resistant Enterococcus strain EC300 with a MIC value of 1.56 µM. Importantly, these bacteriocins could contribute to the ability of S. gallolyticus to colonize the colon where they have been associated with colorectal cancer.Science Foundation Irelan

Phenotypic characterization and genome analysis of a novel Salmonella Typhimurium phage having unique tail fiber genes.

Salmonella enterica serovar Typhimurium is a foodborne pathogen causing occasional outbreaks of enteric infections in humans. Salmonella has one of the largest pools of temperate phages in its genome that possess evolutionary significance for pathogen. In this study, we characterized a novel temperate phage Salmonella phage BIS20 (BIS20) with unique tail fiber genes. It belongs to the subfamily Peduovirinae genus Eganvirus and infects Salmonella Typhimurium strain (SE-BS17; Acc. NO MZ503545) of poultry origin. Phage BIS20 was viable only at biological pH and temperature ranges (pH7 and 37 °C). Despite being temperate BIS20 significantly slowed down the growth of host strain for 24 h as compared to control (P < 0.009). Phage BIS20 features 29,477-base pair (bp) linear DNA genome with 53% GC content and encodes for 37 putative ORFs. These ORFs have mosaic arrangement as indicated by its ORF similarity to various phages and prophages in NCBI. Genome analysis indicates its similarity to Salmonella enterica serovar Senftenberg prophage (SEStP) sequence (Nucleotide similarity 87.7%) and Escherichia virus 186 (~ 82.4% nucleotide similarity). Capsid genes were conserved however those associated with tail fiber formation and assembly were unique to all members of genus Eganvirus. We found strong evidence of recombination hotspot in tail fiber gene. Our study identifies BIS20 as a new species of genus Eganvirus temperate phages as its maximum nucleotide similarity is 82.4% with any phage in NCBI. Our findings may contribute to understanding of origin of new temperate phages.fals