Review: Towards the next-generation models of the rumen microbiome for enhancing predictive power and guiding sustainable production strategies.

The rumen ecosystem harbours a galaxy of microbes working in syntrophy to carry out a metabolic cascade of hydrolytic and fermentative reactions. This fermentation process allows ruminants to harvest nutrients from a wide range of feedstuff otherwise inaccessible to the host. The interconnection between the ruminant and its rumen microbiota shapes key animal phenotypes such as feed efficiency and methane emissions and suggests the potential of reducing methane emissions and enhancing feed conversion into animal products by manipulating the rumen microbiota. Whilst significant technological progress in omics techniques has increased our knowledge of the rumen microbiota and its genome (microbiome), translating omics knowledge into effective microbial manipulation strategies remains a great challenge. This challenge can be addressed by modelling approaches integrating causality principles and thus going beyond current correlation-based approaches applied to analyse rumen microbial genomic data. However, existing rumen models are not yet adapted to capitalise on microbial genomic information. This gap between the rumen microbiota available omics data and the way microbial metabolism is represented in the existing rumen models needs to be filled to enhance rumen understanding and produce better predictive models with capabilities for guiding nutritional strategies. To fill this gap, the integration of computational biology tools and mathematical modelling frameworks is needed to translate the information of the metabolic potential of the rumen microbes (inferred from their genomes) into a mathematical object. In this paper, we aim to discuss the potential use of two modelling approaches for the integration of microbial genomic information into dynamic models. The first modelling approach explores the theory of state observers to integrate microbial time series data into rumen fermentation models. The second approach is based on the genome-scale network reconstructions of rumen microbes. For a given microorganism, the network reconstruction produces a stoichiometry matrix of the metabolism. This matrix is the core of the so-called genome-scale metabolic models which can be exploited by a plethora of methods comprised within the constraint-based reconstruction and analysis approaches. We will discuss how these methods can be used to produce the next-generation models of the rumen microbiome.

Identification of Shiga toxin-producing (STEC) and enteropathogenic (EPEC) Escherichia coli in diarrhoeic calves and comparative genomics of O5 bovine and human STEC.

Escherichia coli producing Shiga toxins (Stx) and the attaching-effacing (AE) lesion (AE-STEC) are responsible for (bloody) diarrhoea in humans and calves while the enteropathogenic E. coli (EPEC) producing the AE lesion only cause non-bloody diarrhoea in all mammals. The purpose of this study was (i) to identify the pathotypes of enterohaemolysin-producing E. coli isolated between 2009 and 2013 on EHLY agar from less than 2 month-old diarrhoeic calves with a triplex PCR targeting the stx1, stx2, eae virulence genes; (ii) to serotype the positive isolates with PCR targeting the genes coding for ten most frequent and pathogenic human and calf STEC O serogroups; and (iii) to compare the MLSTypes and virulotypes of calf and human O5 AE-STEC after Whole Genome Sequencing using two server databases (www.genomicepidemiology.org). Of 233 isolates, 206 were triplex PCR-positive: 119 AE-STEC (58%), 78 EPEC (38%) and 9 STEC (4%); and the stx1+eae+ AE-STEC (49.5%) were the most frequent. Of them, 120 isolates (84% of AE-STEC, 23% of EPEC, 22% of STEC) tested positive with one O serogroup PCR: 57 for O26 (47.5%), 36 for O111 (30%), 10 for O103 (8%) and 8 for O5 (7%) serogroups. The analysis of the draft sequences of 15 O5 AE-STEC could not identify any difference correlated to the host. As a conclusion, (i) the AE-STEC associated with diarrhoea in young calves still belong to the same serogroups as previously (O5, O26, O111) but the O103 serogroup may be emerging, (ii) the O5 AE-STEC from calves and humans are genetically similar.

Breast sharing: New perspectives on an old method.

BACKGROUND: Many techniques have been described for breast reconstruction after mastectomy throughout the decades. In many cases, with excess tissue being discarded, a significant reduction of the contralateral breast was needed for symmetry. Described by Marshall as a one-staged, autologous, non-microsurgical breast reconstruction technique, this method was used in perforator flaps as a breast-sharing technique. METHODS: Between June 2011 and January 2014, the breast-sharing technique was performed in seven patients with simple mastectomy, delayed breast reconstruction, and willingness for autologous non-microsurgical breast reconstruction. All the participants in this study received preoperative oncological screening with ultrasound, magnetic resonance imaging, or mammography, which revealed the absence of pathologic imaging in the donor breast. RESULTS: The experiences of seven patients who underwent breast reconstruction surgery through breast-sharing technique are presented. Due to venous congestion, one of the patients (14%) suffered major complications with total loss of the flap. A total of four patients (57%) incurred minor complications with little to no repercussions on the final outcome. The functional and aesthetic outcomes were very satisfactory, and only one patient required a second touch-up surgery for lipofilling due to unsatisfactory breast volume. Regular follow-ups were done by the oncologist with no recurrences found up to the present. CONCLUSIONS: Using contralateral breast as the donor site, this article presents the first case series for one-stage mammarian reconstruction. With some complications but good aesthetic outcomes, this method has been shown as another available method for breast reconstruction in patients with hypertrophic and ptotic breast.

Two-dimensional magnetotransport in a black phosphorus naked quantum well.

Black phosphorus (bP) is the second known elemental allotrope with a layered crystal structure that can be mechanically exfoliated to atomic layer thickness. Unlike metallic graphite and semi-metallic graphene, bP is a semiconductor in both bulk and few-layer form. Here we fabricate bP-naked quantum wells in a back-gated field effect transistor geometry with bP thicknesses ranging from 6±1 nm to 47±1 nm. Using a polymer encapsulant, we suppress bP oxidation and observe field effect mobilities up to 900 cm(2) V(-1) s(-1) and on/off current ratios exceeding 10(5). Shubnikov-de Haas oscillations observed in magnetic fields up to 35 T reveal a 2D hole gas with Schrödinger fermion character in a surface accumulation layer. Our work demonstrates that 2D electronic structure and 2D atomic structure are independent. 2D carrier confinement can be achieved without approaching atomic layer thickness, advantageous for materials that become increasingly reactive in the few-layer limit such as bP.