Lignocellulosic saccharification by a newly isolated bacterium, Ruminiclostridium thermocellum M3 and cellular cellulase activities for high ratio of glucose to cellobiose

Production of cello-oligosaccharides from corncob residue by degradation-synthesis reactions

The cellulose-rich corncob residue (CCR) is an abundant and renewable agricultural biomass that has been under-exploited. In this study, two strategies were compared for their ability to transform CCR into cello-oligosaccharides (COS). The first strategy employed the use of endo-glucanases. Although selected endo-glucanases from GH9, GH12, GH45, and GH131 could release COS with degrees of polymerization from 2 to 4, the degrading efficiency was low. For the second strategy, first, CCR was efficiently depolymerized to glucose and cellobiose using the cellulase from Trichoderma reesei. Then, using these simple sugars and sucrose as the starting materials, phosphorylases from different microorganisms were combined to generate COS to a level up to 100.3 g/L with different patterns and degrees of polymerization. Using tomato as a model plant, the representative COS obtained from BaSP (a sucrose phosphorylase from Bifidobacterium adolescens), CuCbP (a cellobiose phosphorylase from Cellulomonas uda), and CcCdP (a cellodextrin phosphorylase from Clostridium cellulosi) were shown to be able to promote plant growth. The current study pointed to an approach to make use of CCR for production of the value-added COS. KEY POINTS: • Sequential use of cellulase and phosphorylases effectively generated cello-oligosaccharides from corncob residue. • Cello-oligosaccharides patterns varied in accordance to cellobiose/cellodextrin phosphorylases. • Spraying cello-oligosaccharides promoted tomato growth.

Microbial β-glucosidases: Recent advances and applications

The global β-glucosidase market is currently estimated at ∼400 million USD, and it is expected to double in the next six years; a trend that is mainly ascribed to the demand for the enzyme for biofuel processing. Microbial β-glucosidase, particularly, has thus garnered significant attention due to its ease of production, catalytic efficiency, and versatility, which have all facilitated its biotechnological potential across different industries. Hence, there are continued efforts to screen, produce, purify, characterize and evaluate the industrial applicability of β-glucosidase from actinomycetes, bacteria, fungi, and yeasts. With this rising demand for β-glucosidase, various cost-effective and efficient approaches are being explored to discover, redesign, and enhance their production and functional properties. Thus, this present review provides an up-to-date overview of advancements in the utilization of microbial β-glucosidases as "Emerging Green Tools" in 21st-century industries. In this regard, focus was placed on the use of recombinant technology, protein engineering, and immobilization techniques targeted at improving the industrial applicability of the enzyme. Furthermore, insights were given into the recent progress made in conventional β-glucosidase production, their industrial applications, as well as the current commercial status-with a focus on the patents.

Building microbial consortia to enhance straw degradation, phosphorus solubilization, and soil fertility for rice growth

Straw pollution and the increasing scarcity of phosphorus resources in many regions of China have had severe impacts on the growing conditions for crop plants. Using microbial methods to enhance straw decomposition rate and phosphorus utilization offers effective solutions to address these problems. In this study, a microbial consortium 6 + 1 (consisting of a straw-degrading bacterium and a phosphate-solubilizing bacterium) was formulated based on their performance in straw degradation and phosphorus solubilization. The degradation rate of straw by 6 + 1 microbial consortium reached 48.3% within 7 days (The degradation ability was 7% higher than that of single bacteria), and the phosphorus dissolution rate of insoluble phosphorus reached 117.54 mg·L- 1 (The phosphorus solubilization ability was 29.81% higher than that of single bacteria). In addition, the activity of lignocellulosic degrading enzyme system was significantly increased, the activities of endoglucanase, β-glucosidase and xylanase in the microbial consortium were significantly higher than those in the single strain (23.16%, 28.02% and 28.86%, respectively). Then the microbial consortium was processed into microbial agents and tested in rice pots. The results showed that the microbial agent significantly increased the content of organic matter, available phosphorus and available nitrogen in the soil. Ongoing research focuses on the determination of the effects and mechanisms of a functional hybrid system of straw degradation and phosphorus removal. The characteristics of the two strains are as follows: Straw-degrading bacteria can efficiently degrade straw to produce glucose-based carbon sources when only straw is used as a carbon source. Phosphate-solubilizing bacteria can efficiently use glucose as a carbon source, produce organic acids to dissolve insoluble phosphorus and consume glucose at an extremely fast rate. The analysis suggests that the microbial consortium 6 + 1 outperformed individual strains in terms of both performance and application effects. The two strains within the microbial consortium promote each other during their growth processes, resulting in a significantly higher rate of carbon source consumption compared to the individual strains in isolation. This increased demand for carbon sources within the growth system facilitates the degradation of straw by the strains. At the same time, the substantial carbon consumption during the metabolic process generated a large number of organic acids, leading to the solubilization of insoluble phosphorus. It also provides a basis for the construction of this type of microbial consortium.

Efficient caproic acid production from lignocellulosic biomass by bio-augmented mixed microorganisms

Producing caproic acid via carboxylate platform is an environmentally-friendly approach for treating lignocellulosic agricultural waste. However, its implementation is still challenged by low product yields and selectivity. A microbiome named cellulolytic acid-producing microbiome (DCB), proficient in producing cellulolytic acid, was successfully acquired and shows promise for producing high-level caproic acid. In this study, a bioaugmentation method utilizing Clostridium kluyveri is proposed to enhance caproic acid yield of DCB using rice straw. With exogenous ethanol, bioaugmentation with Clostridium kluyveri significantly improved the caproic acid concentration and selectivity by 7 times and 4.5 times, achieving 12.9 g/L and 55.1 %, respectively. The addition of Clostridium kluyveri introduced reverse β-oxidation pathway, a more efficient caproic acid production pathway. Meanwhile, bioaugmentation enriched the bacteria proficient in degrading straw and producing short-chain fatty acids, providing more substrates for caproic acid production. This study provides potential bioaugmentation strategies for optimizing caproic acid yield from lignocellulosic biomass.

Comparative genomics reveals cellobiose hydrolysis mechanism of Ruminiclostridium thermocellum M3, a cellulosic saccharification bacterium

The cellulosome of Ruminiclostridium thermocellum was one of the most efficient cellulase systems in nature. However, the product of cellulose degradation by R. thermocellum is cellobiose, which leads to the feedback inhibition of cellulosome, and it limits the R. thermocellum application in the field of cellulosic biomass consolidated bioprocessing (CBP) industry. In a previous study, R. thermocellum M3, which can hydrolyze cellulosic feedstocks into monosaccharides, was isolated from horse manure. In this study, the complete genome of R. thermocellum M3 was sequenced and assembled. The genome of R. thermocellum M3 was compared with the other R. thermocellum to reveal the mechanism of cellulosic saccharification by R. thermocellum M3. In addition, we predicted the key genes for the elimination of feedback inhibition of cellobiose in R. thermocellum. The results indicated that the whole genome sequence of R. thermocellum M3 consisted of 3.6 Mb of chromosomes with a 38.9% of GC%. To be specific, eight gene islands and 271 carbohydrate-active enzyme-encoded proteins were detected. Moreover, the results of gene function annotation showed that 2,071, 2,120, and 1,246 genes were annotated into the Clusters of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively, and most of the genes were involved in carbohydrate metabolism and enzymatic catalysis. Different from other R. thermocellum, strain M3 has three proteins related to β-glucosidase, and the cellobiose hydrolysis was enhanced by the synergy of gene BglA and BglX. Meanwhile, the GH42 family, CBM36 family, and AA8 family might participate in cellobiose degradation.

Dynamics of bacterial and archaeal communities during horse bedding and green waste composting

Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.

Biological saccharification coupled with anaerobic digestion using corn straw for sustainable methane production

In this study, accumulated fermentable sugars from biosaccharified corn straw were used to generate methane through anaerobic digestion (AD). The results showed that reducing sugars from biosaccharification expanded corn straw (BECS) treated with Clostridium thermocellum XF811 accumulated with yields of 94.9 mg/g. The BECS used for AD was converted into a high methane yield (7436 mL), which was 49.3 % higher than that of expanded corn straw (ECS). High-throughput microbial analysis suggested that Methanoculleus and Methanobacterium greatly contributed to the high methane yield. Industrial experiments demonstrated that the methane production from BECS by AD was 72,955 m³, which increased by 13.2 % compared to that from ECS. Biosaccharification pretreatment accelerated ECS destruction and accumulated sugars, thereby increasing methane yields. This study provides a strategy for producing clean energy from lignocellulose biomass.

Study on the Sugar-Producing Effect of High-Temperature Anaerobic Straw Biosaccharification Strain

The utilization of straw waste cellulose will be beneficial by economic, social, and environmental means. The present study sought to screen the high-efficiency cellulose sugar-producing strain from corn straw. The 16S high-throughput sequencing method and the combination of morphological, physiological, and biochemical characteristics of the strain confirmed the strain to be Clostridium thermocellum, which was named Clostridium thermocellum FC811. Moreover, the single factor experiment was conducted to investigate the effect of environmental factors on saccharification efficiency. The optimal saccharification conditions of cellulose saccharification of FC811 strain selected through response surface analysis were as follows: temperature of 58.9 °C, pH of 7.21, culture time of 6.60 d, substrate concentration of 5.01 g/L, and yeast powder concentration of 2.15 g/L. The soluble sugar yield was 3.11 g/L, and the conversion rate of reducing sugar was 62.2%. This study will provide a reference for resource and energy utilization of straw materials, simultaneous fermentation of sugar and hydrogen production, and their large-scale production and application.

Effects of diets with various levels of forage rape (Brassica napus) on growth performance, carcass traits, meat quality and rumen microbiota of Hu lambs

BACKGROUND

Apart from being an oil crop, forage rape (Brassica napus) can be used to feed ruminants. The objective of this study was to investigate the effects of pelleted total mixed ration (TMR) diets with various levels of forage rape on growth performance, carcass traits, meat quality, meat nutritional value and rumen microbiota of Hu lambs, which was important for the efficient utilization of forage rape and alleviating the shortage of high-quality forage in China.

RESULTS

Lambs fed on diets with 200-400 g kg^-1 forage rape had greater average daily gain (ADG) and lower feed conversion ratio (FCR) than those fed on diets with 0-100 g kg^-1 of forage rape (P < 0.05). As dietary forage rape levels increased, the content of intramuscular α-linolenic acid and a variety of amino acids in the muscle increased linearly (P < 0.05). No difference was found in carcass traits or meat quality among the dietary treatments (P > 0.05). However, the inclusion of forage rape increased the relative abundance of cellulolytic bacteria and short-chain fatty acid producers, including Succiniclasticum, Fibrobacter and members of the Lachnospiraceae. Besides, Succiniclasticum was found to be positively correlated with the final body weight of lambs.

CONCLUSION

TMR diets that included 200-400 g kg^-1 forage rape could improve the growth performance of lambs, and elevated the content of intramuscular α-linolenic acid and a variety of amino acids in the muscle, accompanied by increased abundance of cellulolytic bacteria in the rumen.

Blue Light Alters the Composition of the Jejunal Microbiota and Promotes the Development of the Small Intestine by Reducing Oxidative Stress

Environmental light has an important impact on the growth, development and oxidative stress of chicks. Thus, we investigated the effects of colored lights on microbes and explored the molecular mechanism by which external color light information alters the gut microbiota and induces the cell response in vivo. We raised 96 chicks under 400-700 nm white (WL), 660 nm red (RL), 560 nm green (GL) or 480 nm blue light (BL) for 42 days. We used 16S rRNA high-throughput pyrosequencing and gas chromatography to explore the effect of different monochromatic lights on the jejunal microbiota. We used qRT-PCR, western blotting, immunohistochemistry and Elisa to determine the effect of different monochromatic lights on small intestine development and oxidative stress levels. With consistency in the upregulation of antioxidant enzyme ability and anti-inflammatory cytokine level, the 16S rRNA and gas chromatography results showed that BL significantly increased the diversity and richness of the jejunal microbiota and improved the relative abundances of Faecalibacterium, Ruminiclostridium_9 and metabolite butyrate content compared with WL, RL and GL (p < 0.05). In addition, we observed that BL increased the goblet cell numbers, PCNA cell numbers, villus-length-to-crypt-depth (V/C) ratios, ZO-1, Occludin, and Claudin-1 protein expression; decreased permeability; and enhanced the digestion and absorption capacity in the jejunum (p < 0.05). In the in vitro experiment, we found that butyrate promoted chick small intestinal epithelial cell (CIEC) proliferation and inhibited apoptosis (p < 0.05). These responses were abrogated by the Gi inhibitor, PI3K inhibitor or AKT inhibitor, but were mimicked by GPR43 agonists or the GSK-3β inhibitor (p < 0.05). Overall, these findings suggested that BL increased the relative abundance of Faecalibacterium, Ruminiclostridium_9 and butyrate production. Butyrate may act as one of the signals to mediate blue-light-induced small intestinal development and mucosal barrier integrity enhancement and promote cell proliferation via the GPR43/Gi/PI3K/AKT/p-GSK-3β/β-catenin pathway.

Microbial mechanism of enhancing methane production from anaerobic digestion of food waste via phase separation and pH control

Phase separation and pH control are commonly used to improve methane production during anaerobic digestion (AD) of food waste, but their influencing mechanisms have not been fully discovered through microbial analysis. In this study, single-phase AD (SPAD), two-phase AD without pH control (TPAD-pHUC), and TPAD with fermentation pH controlled at 6.0 and 4.5 were conducted. The results showed that phase separation decreased the ratio of total bacteria to total archaea in the methanogenic phase. At the organic loading rate (OLR) of 1.9 g/(L·d), methanogenesis was dominated by acetoclastic Methanosaeta in both SPAD and TPAD-pHUC, while elevated Methanoculleus and active hydrogen production initiated a shift from the acetoclastic to hydrogenotrophic pathway in SPAD as OLR increased, eventually resulting in excessive acidification at OLR 3.2 g/(L·d). TPAD-pHUC was dominated by Methanosaeta with scarce hydrogen production genes, and thus maintained a delicate balance between fewer acidogens and methanogens at OLR 3.2-3.7 g/(L·d). TPAD with pH control exhibited higher methane yield (460-482 ml/g) at OLR 1.9 g/(L·d) due to the enhancement of protein degradation and the conversion from methylated compounds to methane by Methanosarcina. High Na⁺ concentration facilitated the proliferation of hydrogen production bacteria, but inhibited acetoclastic methanogenesis at OLR 2.4 g/(L·d). In comparison with SPAD and pH control, TPAD without pH control, integrating 4 d acidogenesis and 22 d methanogenesis, exhibited the best and steady performance at OLR 3.7 g/(L·d) with methane production exceeding 370 ml/g.

Effects of Gasterophilus pecorum infestation on the intestinal microbiota of the rewilded Przewalski's horses in China

Horse botflies have been a threat to the Przewalski’s horses in the Kalamaili Nature Reserve in Xinjiang of China since their reintroduction to the original range. As larvae of these parasites could infest the intestine of a horse for months, they could interact with and alter the structure and composition of its intestinal microbiota, affecting adversely its health. Nonetheless, there are no such studies on the rewilded Przewalski’s horses yet. For the first time, this study characterizes the composition of the intestinal microbiota of 7 rewilded Przewalski’s horses infected severely by Gasterophilus pecorum following and prior to their anthelmintic treatment. Bioinformatics analyses of the sequence data obtained by amplicon high throughput sequencing of bacterial 16S rRNA genes showed that G. pecorum infestation significantly increased the richness of the intestinal microbial community but not its diversity. Firmicutes and Bacteroidetes were found the dominant phyla as in other animals, and the parasitic infestation decreased the F/B ratio largely by over 50%. Large reduction in relative abundances of the two genera Streptococcus and Lactobacillus observed with G. pecorum infestation suggested possible changes in colic and digestion related conditions of the infected horses. Variations on the relative abundance of the genus groups known to be pathogenic or symbiotic showed that adverse impact of the G. pecorum infestation could be associated with reduction of the symbiotic genera Lactobacillus and Bifidobacterium that are probiotics and able to promote immunity against parasitic infection.

Electricity from lignocellulosic substrates by thermophilic Geobacillus species

Given our vast lignocellulosic biomass reserves and the difficulty in bioprocessing them without expensive pretreatment and fuel separation steps, the conversion of lignocellulosic biomass directly into electricity would be beneficial. Here we report the previously unexplored capabilities of thermophilic Geobacillus sp. strain WSUCF1 to generate electricity directly from such complex substrates in microbial fuel cells. This process obviates the need for exogenous enzymes and redox mediator supplements. Cyclic voltammetry and chromatography studies revealed the electrochemical signatures of riboflavin molecules that reflect mediated electron transfer capabilities of strain WSUCF1. Proteomics and genomics analysis corroborated that WSUCF1 biofilms uses type-II NADH dehydrogenase and demethylmenaquinone methyltransferase to transfer the electrons to conducting anode via the redox active pheromone lipoproteins localized at the cell membrane.

Gut microbiota dysbiosis in polycystic ovary syndrome: association with obesity - a preliminary report

The objective was to explore if and how the microbiota changed in polycystic ovary syndrome (PCOS) women compared with healthy women. Eight obese PCOS (PO group), 10 nonobese PCOS (PN group), and nine healthy normal weight women (control) (C group) were enrolled. Insulin (INS), testosterone (T), follicle-stimulating hormone (FSH), luteinizing hormone (LH), estrogen (E2), and dehydroepiandrosterone (DHEA) were detected with radioimmunoassay. Antimullerian hormone (AMH), fasting glucose, and hemoglobin A1c (HbA1c) were determined by a chemiluminescence immunoassay, glucose oxidase method, and HPLC, respectively. Gut microbiota composition was evaluated by PCR. Alpha diversity was assessed using Chao1 and the Shannon index. PCOS women showed significantly higher T, LH, and LH/FSH and lower FSH levels than the C group (p < 0.05). The AMH level was significantly higher in the PO than in the PN group (p < 0.05). The PO group presented a significantly higher fasting INS level and HMOA-IR scores than the other groups, lower observed SVs and alpha diversity than the C group, higher beta diversity than the PN group (p < 0.05), and decreased abundances of genera (mainly butyrate producers). Regression analysis showed that decreased abundances of several genera were correlated with higher circulating T and impaired glucose metabolism. PCOS is associated with changes in the gut microbiota composition. Obesity has a driving role in the development of dysbiotic gut microbiota in PCOS.

Isolation of Thermostable Lignocellulosic Bacteria From Chicken Manure Compost and a M42 Family Endocellulase Cloning From Geobacillus thermodenitrificans Y7

The composting ecosystem provides a potential resource for finding new microorganisms with the capability for cellulose degradation. In the present study, Congo red method was used for the isolating of thermostable lignocellulose-degrading bacteria from chicken manure compost. A thermophilic strain named as Geobacillus thermodenitrificans Y7 with acid-resident property was successfully isolated and employed to degrade raw switchgrass at 60°C for 5 days, which resulted in the final degradation rates of cellulose, xylan, and acid-insoluble lignin as 18.64, 12.96, and 17.21%, respectively. In addition, GC-MS analysis about aromatic degradation affirm the degradation of lignin by G. thermodenitrificans Y7. Moreover, an endocellulase gene belong to M42 family was successfully cloned from G. thermodenitrificans Y7 and expressed in Escherichia coli BL21. Recombinant enzyme Cel-9 was purified by Ni-NTA column based the His-tag, and the molecular weight determined as 40.4 kDa by SDA-PAGE. The characterization of the enzyme Cel-9 indicated that the maximum enzyme activity was realized at 50°C and pH 8.6 and, Mn2+ could greatly improve the CMCase enzyme activity of Cel-9 at 10 mM, which was followed by Fe2+ and Co2+. Besides, it also found that the β-1,3-1,4, β-1,3, β-1,4, and β-1,6 glucan linkages all could be hydrolyzed by enzyme Cel-9. Finally, during the application of enzyme Cel-9 to switchgrass, the saccharification rates achieved to 1.81 ± 0.04% and 2.65 ± 0.03% for 50 and 100% crude enzyme, respectively. All these results indicated that both the strain G. thermodenitrificans Y7 and the recombinant endocellulase Cel-9 have the potential to be applied to the biomass industry.

L-Arginine and N-carbamoylglutamic acid supplementation enhance young rabbit growth and immunity by regulating intestinal microbial community

Objective

An experiment was conducted to determine the effects of L-arginine (L-Arg) and N-carbamoylglutamic acid (NCG) on the growth, metabolism, immunity and community of cecal bacterial flora of weanling and young rabbits.

Methods

Eighteen normal-grade male weanling Japanese White rabbits (JWR) were selected and randomly divided into 6 groups with or without L-Arg and NCG supplementation. The whole feeding process was divided into weanling stage (day 37 to 65) and young stage (day 66 to 85). The effects of L-Arg and NCG on the growth, metabolism, immunity and development of the ileum and jejunum were compared via nutrient metabolism experiments and histological assessment. The different communities of cecal bacterial flora affected by L-Arg and NCG were assessed using high-throughput sequencing technology and bioinformatics analysis.

Results

The addition of L-Arg and NCG enhanced the growth of weanling and young rabbit by increasing the nitrogen metabolism, protein efficiency ratio, and biological value, as well as feed intake and daily weight gain. Both L-Arg and NCG increased the concentration of immunoglobulin A (IgA), IgM, and IgG. NCG was superior to L-Arg in promoting intestinal villus development by increasing villus height, villus height/crypt depth index, and reducing the crypt depth. The effects of L-Arg and NCG on the cecal bacterial flora were mainly concentrated in different genera, including Parabacteroides, Roseburia, dgA-11_gut_group, Alistipes, Bacteroides, and Ruminococcaceae_UCG-005. These bacteria function mainly in amino acid transport and metabolism, energy production and conversion, lipid transport and metabolism, recombination and repair, cell cycle control, cell division, and cell motility.

Conclusion

L-Arg and NCG can promote the growth and immunity of weanling and young JWR, as well as effecting the jejunum and ileum villi. L-Arg and NCG have different effects in the promotion of nutrient utilization, relieving inflammation and enhancing adaptability through regulating microbial community.

Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken

The gut microbiota is crucial for metabolic homeostasis, immunity, growth and overall health, and it is recognized that early-life microbiota acquisition is a pivotal event for later-life health. Recent studies show that gut microbiota diversity and functional activity are synchronized with the host circadian rhythms in healthy individuals, and circadian disruption elicits dysbiosis in mammalian models. However, no studies have determined the associations between circadian disruption in early life, microbiota colonization, and the consequences for microbiota structure in birds. Chickens, as a major source of protein around the world, are one of the most important agricultural species, and their gut and metabolic health are significant concerns. The poultry industry routinely employs extended photoperiods (>18 h light) as a management tool, and their impacts on the chicken circadian, its role in gut microbiota acquisition in early life (first 3 weeks of life), and consequences for later life microbiota structure remain unknown. In this study, the objectives were to (a) characterize circadian activity under two different light regimes in layer chicken (12/12 h′ Light/Dark (LD) and 23/1 h LD), (b) characterize gut microbiota acquisition and composition in the first 4 weeks of life, (c) determine if gut microbiota oscillate in synchrony with the host circadian rhythm, and (d) to determine if fecal microbiota is representative of cecal microbiota in early life. Expression of clock genes (clock, bmal1, and per2) was assayed, and fecal and cecal microbiotas were characterized using 16S rRNA gene amplicon analyses from birds raised under two photoperiod treatments. Chickens raised under 12/12 LD photoperiods exhibited rhythmic clock gene activity, which was absent in birds raised under the extended (23/1 LD) photoperiod. There was differential microbiota acquisition under different photoperiod regimes in newly hatched chicks. Gut microbiota members showed a similar oscillating pattern as the host, but this association was not as strong as found in mammals. Finally, the fecal microbiota was found to be not representative of cecal microbiota membership and structure in young birds. This is one of the first studies to demonstrate the use of photoperiods to modulate microbiota acquisition in newly hatched chicks, and show their potential as a tool to promote the colonization of beneficial microorganisms.

High-throughput sequencing reveals the effect of Bacillus subtilis CGMCC 1.921 on the cecal microbiota and gene expression in ileum mucosa of laying hens

This study evaluated the effects of Bacillus subtilis CGMCC 1.921 supplementation on the production performance, cecal microbiota and mucosal transcriptome of laying hens by 16s rRNA gene sequencing and RNA-seq. A total of 144 27-week-old Hy-Line Brown laying hens were allocated into two treatments, namely, a basal diet without additions (T0) and the basal diet supplemented with 1.0 × 108 cfu/g (T1) B. subtilis CGMCC 1.921, with six replicates of 12 birds in each for 24 weeks. The results showed that T1 significantly decreased feed:egg ratio compared with T0 (P < 0.05). Dietary supplementation with B. subtilis CGMCC 1.921 increased the Shannon index (P < 0.05) which indicated enhanced diversity of cecal microflora. An increasing trend in Observed species index (P = 0.072) was observed in hens fed with diets supplemented with B. subtilis CGMCC 1.921 that showed a higher species richness. And T1 modulated cecal microbiota by increasing the relative proportion of Alistipes, Subdoligranulum, Ruminococcaceae UCG-014, Anaerotruncus, Ruminiclostridium 5, Ruminococcaceae UCG-010, Erysipelatoclostridium, Ruminococcaceae UCG-009, Family XIII AD3011 group, Bacillus, Faecalicoccus, Firmicutes bacterium CAG822, Oxalobacter, and Dielma at genus level (P < 0.05). In addition, there was a tendency of increase in the relative abundance of Lactobacillus (P = 0.055), Anaerobiospirillum (P = 0.059) and Family XIII UCG-001 (P = 0.054), Peptococcus (P = 0.078), and Ruminococcaceae UCG-004 (P = 0.078). Moreover, heatmap analysis indicated that the abundance of Campylobacter and Clostridium sensu stricto 1 was lower than T0. A total of 942 genes were identified by differential expression analysis, among which 400 genes were upregulated and 542 genes were downregulated. Bioinformatics analysis suggested that the upregulated genes were involved in Peroxisome Proliferator Activated Receptor (PPAR) signaling pathway, starch and sucrose metabolism, glycine/serine/threonine metabolism, and galactose metabolism, which may promote nutrient absorption. This study provided novel insights into the probiotic mechanisms of B. subtilis on laying hens.

Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities

Rhodothermaceae bacterium RA is a halo-thermophile isolated from a saline hot spring. Previously, the genome of this bacterium was sequenced using a HiSeq 2500 platform culminating in 91 contigs. In this report, we report on the resequencing of its complete genome using a PacBio RSII platform. The genome has a GC content of 68.3%, is 4,653,222 bp in size, and encodes 3711 genes. We are interested in understanding the carbohydrate metabolic pathway, in particular the lignocellulosic biomass degradation pathway. Strain RA harbors 57 glycosyl hydrolase (GH) genes that are affiliated with 30 families. The bacterium consists of cellulose-acting (GH 3, 5, 9, and 44) and hemicellulose-acting enzymes (GH 3, 10, and 43). A crude cell-free extract of the bacterium exhibited endoglucanase, xylanase, β-glucosidase, and β-xylosidase activities. The complete genome information coupled with biochemical assays confirms that strain RA is able to degrade cellulose and xylan. Therefore, strain RA is another excellent member of family Rhodothermaceae as a repository of novel and thermostable cellulolytic and hemicellulolytic enzymes.

Fenton pre-treatment of rice straw with citric acid as an iron chelate reagent for enhancing saccharification

Rice straw was pre-treated by Fenton action with citric acid for chelation; the pre-treated rice straw was saccharified byRuminiclostridium thermocellumM3.

Enhanced saccharification of cellulose and sugarcane bagasse by Clostridium thermocellum cultures with Triton X-100 and β-glucosidase/Cellic®CTec2 supplementation

Increased saccharification and utilization of biomass directly byC. thermocellumcultures with Triton X-100 and β-glucosidase supplementation.

Biorefinery cascade processing for creating added value on tomato industrial by-products from Tunisia

BACKGROUND

In today's consumer perception of industrial processes and food production, aspects like food quality, human health, environmental safety, and energy security have become the keywords. Therefore, much effort has been extended toward adding value to biowastes of agri-food industries through biorefinery processing approaches. This study focused, for the first time, on the valorization of tomato by-products of a Tunisian industry for the recovery of value-added compounds using biorefinery cascade processing.

RESULTS

The process integrated supercritical CO₂ extraction of carotenoids within the oil fractions from tomato seeds (TS) and tomato peels (TP), followed by a batch isolation of protein from the residues. The remaining lignocellulosic matter from both fractions was then submitted to a liquid hot water (LHW) hydrolysis. Supercritical CO₂ experiments extracted 5.79% oleoresin, 410.53 mg lycopene/kg, and 31.38 mg β-carotene/kg from TP and 26.29% oil, 27.84 mg lycopene/kg, and 5.25 mg β-carotene/kg from TS, on dry weights. Protein extraction yields, nearing 30% of the initial protein contents equal to 13.28% in TP and 39.26% in TS, revealed that TP and TS are a rich source of essential amino acids. LHW treatment run at 120-200 °C, 50 bar for 30 min showed that a temperature of 160 °C was the most convenient for cellulose and hemicellulose hydrolysis from TP and TS, while keeping the degradation products low.

CONCLUSIONS

Results indicated that tomato by-products are not only a green source of lycopene-rich oleoresin and tomato seed oil (TSO) and of protein with good nutritional quality but also a source of lignocellulosic matter with potential for bioethanol production. This study would provide an important reference for the concept and the feasibility of the cascade fractionation of valuable compounds from tomato industrial by-products.Graphical abstractSchema of biorefinery cascade processing of tomato industrial by-products toward isolation of valuable fractions.