Maceration of Clover and Grass Leaves by Lachnospira multiparus

Complete genome sequence of Sphingobium sp. strain PAMC 28499 reveals a potential for degrading pectin with comparative genomics approach

BACKGROUND

Spingobium sp. PAMC 28499 is isolated from the glaciers of Uganda. Uganda is a unique region where hot areas and glaciers coexist, with a variety of living creatures surviving, but the survey on them is very poor. The genetic character and complete genome information of Sphingobium strains help with environmental studies and the development of better to enzyme industry.

OBJECTIVE

In this study, complete genome sequence of Spingobium sp. PAMC 28499 and comparative analysis of Spingobium species strains isolated from variety of the region.

METHODS

Genome sequencing was performed using PacBio sequel single-molecule real-time (SMRT) sequencing technology. The predicted gene sequences were functionally annotated and gene prediction was carried out using the program NCBI non-redundant database. And using dbCAN2 and KEGG data base were degradation pathway predicted and protein prediction about carbohydrate active enzymes (CAZymes).

RESULTS

The genome sequence has 64.5% GC content, 4432 coding protein coding genes, 61 tRNAs, and 12 rRNA operons. Its genome encodes a simple set of metabolic pathways relevant to pectin and its predicted degradation protein an unusual distribution of CAZymes with extracellular esterases and pectate lyases. CAZyme annotation analyses revealed 165 genes related to carbohydrate active, and especially we have found GH1, GH2, GH3, GH38, GH35, GH51, GH51, GH53, GH106, GH146, CE12, PL1 and PL11 such as known pectin degradation genes from Sphingobium yanoikuiae. These results confirmed that this Sphingobium sp. strain PAMC 28499 have similar patterns to RG I pectin-degrading pathway.

CONCLUSION

In this study, isolated and sequenced the complete genome of Spingobium sp. PAMC 28499. Also, this strain has comparative genome analysis. Through the complete genome we can predict how this strain can store and produce energy in extreme environment. It can also provide bioengineered data by finding new genes that degradation the pectin.

Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon

Pectin is abundant in modern day diets, as it comprises the middle lamellae and one-third of the dry carbohydrate weight of fruit and vegetable cell walls. Currently there is no specialized model organism for studying pectin fermentation in the human colon, as our collective understanding is informed by versatile glycan-degrading bacteria rather than by specialist pectin degraders. Here we show that the genome of Monoglobus pectinilyticus possesses a highly specialized glycobiome for pectin degradation, unique amongst Firmicutes known to be in the human gut. Its genome encodes a simple set of metabolic pathways relevant to pectin sugar utilization, and its predicted glycobiome comprises an unusual distribution of carbohydrate-active enzymes (CAZymes) with numerous extracellular methyl/acetyl esterases and pectate lyases. We predict the M. pectinilyticus degradative process is facilitated by cell-surface S-layer homology (SLH) domain-containing proteins, which proteomics analysis shows are differentially expressed in response to pectin. Some of these abundant cell surface proteins of M. pectinilyticus share unique modular organizations rarely observed in human gut bacteria, featuring pectin-specific CAZyme domains and the cell wall-anchoring SLH motifs. We observed M. pectinilyticus degrades various pectins, RG-I, and galactan to produce polysaccharide degradation products (PDPs) which are presumably shared with other inhabitants of the human gut microbiome (HGM). This strain occupies a new ecological niche for a primary degrader specialized in foraging a habitually consumed plant glycan, thereby enriching our understanding of the diverse community profile of the HGM.

Alkaline hydrogen peroxide treatment unlocks energy in agricultural by-products

Lignocellulosic residues (wheat straw, corncobs, and cornstalks) were treated with a dilute alkaline solution of hydrogen peroxide and suspended in cattle rumen in situ to measure microbial degradation. The rate and extent of dry matter disappearance were markedly increased as a result of the treatment. Results in vivo indicate that this treatment increases the fermentability of wheat straw structural carbohydrates such that this agricultural by-product may be considered an acceptable energy source for the ruminant animal. Treatment of wheat straw allowed more complete bacterial colonization and more rapid degradation of the cell wall.

Degradation of forage chicory by ruminal fibrolytic bacteria

AIMS

Determine the susceptibility of forage chicory (Cichorium intybus L.) to degradation by ruminal fibrolytic bacteria and measure the effects on cell-wall pectic polysaccharides.

METHODS AND RESULTS

Large segments of fresh forage chicory were degraded in vitro by Lachnospira multiparus and Fibrobacter succinogenes, but not by Ruminococcus flavefaciens or Butyrivibrio hungatei. Cell-wall pectins were degraded extensively (95%) and rapidly by L. multiparus with a simultaneous release of uronic acids and the pectin-derived neutral monosaccharides arabinose, galactose and rhamnose. Fibrobacter succinogenes also degraded cell-wall pectins extensively, but at a slower rate than L. multiparus. Immunofluorescence microscopy using monoclonal antibodies revealed that, after incubation, homogalacturonans with both low and high degrees of methyl esterification were almost completely lost from walls of all cell types and from the middle lamella between cells.

CONCLUSIONS

Only two of the four ruminal bacteria with pectinolytic activity degraded fresh chicory leaves, and each showed a different pattern of pectin breakdown. Degradation was greatest for F. succinogenes which also had cellulolytic activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The finding of extensive removal of pectic polysaccharides from the middle lamella and the consequent decrease in particle size may explain the decreased rumination and the increased intake observed in ruminants grazing forage chicory.

Degradation of barley straw, ryegrass, and alfalfa cell walls by Clostridium longisporum and Ruminococcus albus

The recently isolated ruminal sporeforming cellulolytic anaerobe Clostridium longisporum B6405 was examined for its ability to degrade barley straw, nonlignified cell walls (mesophyll and epidermis) and lignified cell walls (fiber) of ryegrass, and alfalfa cell walls in comparison with strains of Ruminococcus albus. R. albus strains degraded 20 to 28% of the dry matter in barley straw in 10 days, while the clostridium degraded less than 2%. A combined inoculum of R. albus SY3 and strain B6405 was no more efficient than SY3 alone, and the presence of Methanobacterium smithii PS did not increase the amount of dry matter degraded. In contrast, with alfalfa cell walls as the substrate, the clostridium was twice as active (28% weight loss) as R. albus SY3 (15%). The percentages of dry matter degraded from ryegrass cell walls of mesophyll, epidermis, and fiber for the clostridium were 50, 47, and 32%, respectively, and for R. albus SY3 they were 77, 73, and 63%, respectively. Analyses of the predominant neutral sugars (arabinose, xylose, and glucose) in the plant residues after bacterial attack were consistent with the values for dry matter weight loss. Measurements of the amount of carbon appearing in the fermentation products indicated that R. albus SY3 degraded ryegrass mesophyll cell walls most rapidly, with epidermis and fiber cell walls being degraded at similar rates. Strain B6405 attacked alfalfa cell walls at a rate greater than that of any of the ryegrass substrates. These results indicate an unexpected degree of substrate specificity in the ability of C. longisporum to degrade plant cell wall material.

Bloat in sheep (Ovis aries)

1. Most of the field studies on bloat are conducted with cattle and most of the laboratory experiments seeking to explain the various parameters associated with bloat are done with sheep. 2. Based on grazing behaviour, it would be expected that sheep might bloat more severely than cattle because they selectively choose to eat leaves over stems and chew what they ingest more frequently than cattle. Furthermore, sheep appear to select legumes over grasses because the legumes can be eaten more rapidly. However, because they are selective, sheep eat more slowly than cattle. Despite a higher bloat expectation, bloating in sheep is reported to be less of a problem than in cattle. 3. Although frothing of rumen ingesta was described earlier in cattle as the cause of acute legume bloat, experiments with frothy bloat in sheep preceded those in cattle. 4. Anti-frothing agents were used in sheep before cattle to treat acute legume bloat. 5. Experiments devoted to the study of eructation in ruminants were carried out on sheep, then cattle. 6. Convincing evidence that rumen motility does not cease during acute legume bloat was gathered using sheep. 7. Although the transected tracheal technique for the determination of the volume of eructated gas was developed with cattle, the pathway of eructated gas was confirmed with sheep. 8. All the current evidence accumulated from experiments with sheep supports the hypothesis that death due to legume bloat is caused by acute neural, respiratory, and cardiovascular insult resulting from the effect of the distended rumen on thoracic viscera, diaphragm, intercostal muscles, and the abdominal vena cava. 9. Experiments with sheep and cattle being fed scabrous and nonscabrous diets similar in chemical composition show that sheep are more resistant than cattle to the increase in intrarumen pressure, decline in rumen contraction amplitude, and decrease in rumen contraction frequency caused by nonscabrous diets. 10. The sequence of events in the reticulorumen during primary and secondary contractions previously described following visual and palpation experiments with cattle was confirmed by the use of myoelectrodes implanted in the various sacs of the reticulorumen of sheep. 11. Elevated intrarumen pressure is associated with an increase in the frequency of primary (mixing) and secondary (eructation) contractions (more secondaries than primaries).(ABSTRACT TRUNCATED AT 400 WORDS)

Microbial ecology and activities in the rumen: part 1

This review describes the progress which has been made during the last 10 to 15 years in the field of rumen microbiology. It is basically an account of new discoveries in the bacteriology, protozoology, biochemistry, and ecology of the rumen microbial population. As such it covers a wide range of subjects including the isolation and properties of methanogenic bacteria, the role of rumen phycomycete fungi, anaerobic energy conservation, and general metabolic aspects of rumen microorganisms. It also attempts, however, to describe and develop new concepts in rumen microbiology. These consist principally of interactions of the microbemicrobe, microbe-food and microbe-host types, and represent the main areas of recent advance in our understanding of the rumen ecosystem. The development of experimental techniques such as chemostat culture and scanning electron microscopy are shown to have been instrumental in progress in these areas. The paper is concluded with an assessment of our present knowledge of the rumen fermentation, based on the degree of success of experiments with gnotobiotic ruminants inoculated with defined flora and in mathematical modeling of the fermentation. The efficacy of chemical manipulation of the fermentation in ruminant is also discussed in this light.

Sequence of Events in the Digestion of Fresh Legume Leaves by Rumen Bacteria

When fresh whole leaves of six different species of forage legumes were suspended in an artificial rumen medium and inoculated with rumen bacteria, bacterial adhesion and proliferation were noted at the stomata, and penetration of the stomate by these bacteria was documented by electron microscopy. The invading bacteria adhered to surfaces within the intercellular space of the leaf and produced very extensive exopolysaccharide-enclosed microcolonies. After some of the legume leaf cell walls were disorganized and ruptured by bacterial digestion, these cells (notably, parenchyma and epidermal cells) were invaded by bacteria, with subsequent formation of intracellular microcolonies. However, other cells were neither ruptured nor colonized (notably, stomata guard cells and vascular tissue). At all stages of the digestion of intact legume leaves, the rumen bacteria grew in microcolonies composed of cells of single or mixed morphological types, and a particular ecological niche was often completely and consistently occupied by a very large microcolony of cells of single or mixed morphological types.