Monoglobus pectinilyticus gen. nov., sp. nov., a pectinolytic bacterium isolated from human faeces

Effects of herbal dregs supplementation of Salvia miltiorrhiza and Isatidis Radix residues improved production performance and gut microbiota abundance in late-phase laying hens

The present study was designed to evaluate the effect of a mixture of Chinese medicinal residues (CMRs) consisting of Salvia miltiorrhiza residues (SMR) and Isatidis Radix residues (IRR) on productive performance, egg quality, serum lipid and hormone levels, liver and blood antioxidant capacity, oviduct inflammation levels, and gut microbiota in the late-laying stage. A total of 288 fifty-four-week-old BaShang long-tailed hens were divided into four groups. The feed trial period was 8 weeks. The control group was fed the basic diet as a CCMR group, supplemented with 3, 4, and 6% for the experimental groups LCMR, MCMR, and HCMR. The egg production rate of the MCMR group was 8.1% higher than that of the CCMR group (p < 0.05). Serum triglyceride (TG) levels of hens of the CMR-supplemented group were significantly decreased than those of the CCMR group (p < 0.05). The group supplemented with different levels of CMR had significantly higher serum HDL-C levels compared with the control group (p < 0.05). Follicle-stimulating hormone (FSH) and luteinizing hormone (LH) levels were remarkably increased for the LCMR and MCMR groups and significantly decreased for the HCMR group compared to CCMR (p < 0.05). Serum and liver glutathione peroxidase (GSH-PX) activities were significantly increased, and malondialdehyde (MDA) levels were significantly decreased in the MCMR group compared to the CCMR group (p < 0.05). The expression levels of tubal inflammatory factor markers (IL-4, IL-1β, TNF-α) in the MCMR and HCMR groups were consistent with the pathological findings of the sections. As for cecal microbiota, supplementation with CMR affected the alpha diversity of the cecum microbiome at the genus level. The Shannon index was significantly higher in the MCMR group than in the CCMR and HCMR groups (p < 0.05). Supplementation with different levels of CMR mainly regulated the ratio of intestinal Firmicutes to Bacteroidetes and the abundance of phyla such as Proteobacteria. In addition, CMR supplementation at different levels in the diet enriched lipid-metabolizing bacteria, such as Bacteroides and Ruminococcus_gnavus_group. Furthermore, according to linear discriminant analysis (LDA) effect size (LEfSe) analysis, the MCMR group showed an increase in the number of short-chain fatty acid-producing bacteria Romboutsia and fiber-degrading specialized bacteria Monoglobus. Therefore, supplementation of appropriate amounts of CMR to the diet of laying hens enhanced reproductive hormone levels, hepatic antioxidant capacity, and lipid metabolism, alleviated the levels of oviductal inflammatory factors, and modulated the abundance structure of bacterial flora to improve the late-laying performance and egg quality. The results of the current study showed that CMR is a beneficial feed supplement for chickens when added in moderation.

An overview of microbial enzymatic approaches for pectin degradation

Pectin, a complex natural macromolecule present in primary cell walls, exhibits high structural diversity. Pectin is composed of a main chain, which contains a high amount of partly methyl-esterified galacturonic acid (GalA), and numerous types of side chains that contain almost 17 different monosaccharides and over 20 different linkages. Due to this peculiar structure, pectin exhibits special physicochemical properties and a variety of bioactivities. For example, pectin exhibits strong bioactivity only in a low molecular weight range. Many different degrading enzymes, including hydrolases, lyases and esterases, are needed to depolymerize pectin due to its structural complexity. Pectin degradation involves polygalacturonases/rhamnogalacturonases and pectate/pectin lyases, which attack the linkages in the backbone via hydrolytic and β-elimination modes, respectively. Pectin methyl/acetyl esterases involved in the de-esterification of pectin also play crucial roles. Many α-L-rhamnohydrolases, unsaturated rhamnogalacturonyl hydrolases, arabinanases and galactanases also contribute to heterogeneous pectin degradation. Although numerous microbial pectin-degrading enzymes have been described, the mechanisms involved in the coordinated degradation of pectin through these enzymes remain unclear. In recent years, the degradation of pectin by Bacteroides has received increasing attention, as Bacteroides species contain a unique genetic structure, polysaccharide utilization loci (PULs). The specific PULs of pectin degradation in Bacteroides species are a new field to study pectin metabolism in gut microbiota. This paper reviews the scientific information available on pectin structural characteristics, pectin-degrading enzymes, and PULs for the specific degradation of pectin.

Gastrointestinal Fermentable Polysaccharide Is Beneficial in Alleviating Loperamide-Induced Constipation in Mice

To investigate the role of gastrointestinal (GI) polysaccharide fermentation in alleviating constipation, two polysaccharide fractions were isolated from a soluble fiber extract with determined anti-constipation activity: a 2.04 kDa neutral fraction (SSP-1) contained 99.29% glucose, and a 41.66 kDa acidic fraction (SSP-2) contained 63.85% uronic acid. After mice were given loperamide for 14 d to induce constipation, the GI transit rate increased significantly in the SSP-1 group (p < 0.05) but not in the SSP-2 group. The stool weight in the SSP-2 group was significantly higher than that in SSP-1 (383.60 mg vs. 226.23 mg) (p < 0.05). Both SSP-1 and SSP-2 groups had significantly increased serum gastrin and motilin levels (p < 0.05) and changes in their fecal short-chain fatty acid (SCFA) profiles, while SSP-1 showed better fermentation properties than SSP-2 in terms of statistically higher fecal contents of acetic acid and total SCFAs (p < 0.05). Bioinformatic analysis indicated that SSP-1 upregulated bacteria such as Oscillibacter to improve SCFA metabolism and stimulate GI hormone secretion, while SSP-2 had less influence on the gut microbiota. These results suggest that the neutral polysaccharide with superior GI fermentation properties exerted beneficial effects on constipation, while the less fermentable pectic fraction might act as a stool-bulking agent.

The digestive behavior of pectin in human gastrointestinal tract: a review on fermentation characteristics and degradation mechanism

Pectin is widely spread in nature and it develops an extremely complex structure in terms of monosaccharide composition, glycosidic linkage types, and non-glycosidic substituents. As a non-digestible polysaccharide, pectin exhibits resistance to human digestive enzymes, however, it is easily utilized by gut microbiota in the large intestine. Currently, pectin has been exploited as a novel functional component with numerous physiological benefits, and it shows a promising prospect in promoting human health. In this review, we introduce the regulatory effects of pectin on intestinal inflammation and metabolic syndromes. Subsequently, the digestive behavior of pectin in the upper gastrointestinal tract is summarized, and then it will be focused on pectin's fermentation characteristics in the large intestine. The fermentation selectivity of pectin by gut bacteria and the effects of pectin structure on intestinal microecology were discussed to highlight the interaction between pectin and bacterial community. Meanwhile, we also offer information on how gut bacteria orchestrate enzymes to degrade pectin. All of these findings provide insights into pectin digestion and advance the application of pectin in human health.

Association between gut microbiota and anxiety symptoms: A large population-based study examining sex differences

BACKGROUND

This study aimed to examine the association between anxiety symptoms and gut microbial composition and to infer their functional pathways.

METHODS

In total, 605 participants were included in this study. Participants were categorized into anxious and non-anxious groups according to their Beck Anxiety Inventory scores, and their fecal microbiota was profiled using 16S ribosomal RNA gene sequencing. The microbial diversity and taxonomic profiles of the participants with anxiety symptoms were analyzed using generalized linear models. The function of the gut microbiota was inferred by comparing 16S rRNA data between the anxious and non-anxious groups.

RESULTS

The gut microbiome of the anxious group showed lower alpha diversity than that of the non-anxious group, and there were prominent differences in the community structure of the gut microbiota between the two groups. Male participants with anxiety had lower relative abundances of the family Oscillospiraceae, fibrolytic bacteria including those of the family Monoglobaceae, and short-chain fatty acid-producing bacteria such as those of the genus Lachnospiraceae_NK4A136 than those without anxiety symptoms. Female participants with anxiety symptoms had a lower relative abundance of the genus Prevotella than those without anxiety symptoms.

LIMITATION

The direction of causality between anxiety symptoms and the gut microbiota was unclear owing to the cross-sectional design of the study.

CONCLUSION

Our results elucidate the association between anxiety symptoms and gut microbiota and provide insights for developing interventions to treat anxiety symptoms.

S-(-)-Oleocanthal Ex Vivo Modulatory Effects on Gut Microbiota

Compelling evidence points to the critical role of bioactive extra-virgin olive oil (EVOO) phenolics and gut microbiota (GM) interplay, but reliable models for studying the consequences thereof remain to be developed. Herein, we report an optimized ex vivo fecal anaerobic fermentation model to study the modulation of GM by the most bioactive EVOO phenolic S-(-)-oleocanthal (OC), and impacts therefrom, focusing on OC biotransformation in the gut. This model will also be applicable for characterization of GM interactions with other EVOO phenolics, and moreover, for a broadly diverse range of bioactive natural products. The fecal fermentation media and time, and mouse type and gender, were the major factors varied and optimized to provide better understanding of GM-OC interplay. A novel resin entrapment technique (solid-phase extraction) served to selectively entrap OC metabolites, degradation products, and any remaining fraction of OC while excluding interfering complex fecal medium constituents. The effects of OC on GM compositions were investigated via shallow shotgun DNA sequencing. Robust metabolome analyses identified GM bacterial species selectively altered (population numbers/fraction) by OC. Finally, the topmost OC-affected gut bacterial species of the studied mice were compared with those known to be extant in humans and distributions of these bacteria at different human body sites. OC intake caused significant quantitative and qualitative changes to mice GM, which was also comparable with human GM. Results clearly highlight the potential positive health outcomes of OC as a prospective nutraceutical.

The impact of different diets and genders on fecal microbiota in Hanwoo cattle

Bovine fecal microbiota is important for host health and its composition can be affected by various factors, such as diet, age, species, breed, regions, and environments. The objective of this study was to evaluate the impact of diet and gender on fecal microbiota in Korean native Hanwoo cattle. The 16S rRNA gene amplicon sequencing of fecal microbiota was conducted from 44 Hanwoo cattle divided into four groups: (1) 11 heifers fed an oat hay plus total mixed ration (TMR) diet for breeding (HOTB), (2) 11 heifers fed an early fattening TMR diet (HEFT), (3) 11 steers fed the early fattening TMR diet (SEFT), and (4) 11 steers fed the late fattening TMR diet (SLFT). Firmicutes and Bacteroidota were the first and second most dominant phyla in all the samples, respectively. The Firmicutes/Bacteroidota (F/B) ratio associated with feed efficiency was significantly greater in the SLFT group than in the other groups. At the genus level, Romboutsia, Paeniclostridium, and Turicibacterwere the most abundant in the SLFT while Akkermansia, Bacteroides, and Monoglobus were the most abundant in the HOTB group. Although the same early fattening TMR diet was fed to Hanwoo heifers and steers, Marvinbryantia and Coprococcus were the most abundant in the HEFT group while Alistipes and Ruminococcus were the most abundant in the SEFT group. Shannon and Simpson diversity indices were significantly lower in the SLFT group than in the other groups. Distribution of fecal microbiota and functional genetic profiles were significantly different among the four treatment groups. The present study demonstrates that different diets and genders can affect fecal microbiota and the F/B ratio may be associated with feed efficiency in Hanwoo cattle. Our results may help develop strategies to improve gut health and productivity through manipulation of fecal microbiota using the appropriate diet considering Hanwoo cattle gender.

Exploration and comparison of bacterial communities present in bovine faeces, milk and blood using 16S rRNA metagenomic sequencing

Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial communities forming a complex ecosystem of niches. We aimed to explore and compare the faecal, milk and blood microbiota of cows through 16S rRNA sequencing. All downstream analyses were performed using applications in R Studio (v3.6.1). Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but non-significant between blood and milk using Kruskal-Wallis test, P < 0,05. The beta-diversity metrics on Principal Coordinate Analysis and Non-Metric Dimensional Scaling significantly clustered samples by type (PERMANOVA test, P < 0,05). The overall analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. Firmicutes, Bacteroidota and Proteobacteria were the most abundant phyla overall. A total of 58 genus-level taxa occurred concurrently between the body sites. The important taxa could be categorized into four potentially pathogenic clusters i.e. arthropod-borne; food-borne and zoonotic; mastitogenic; and metritic and abortigenic. A number of taxa were significantly differentially abundant (DA) between sites based on the Wald test implemented in DESeq2 package. Majority of the DA taxa (i.e. Romboutsia, Paeniclostridium, Monoglobus, Akkermansia, Turicibacter, Bacteroides, Candidatus_Saccharimonas, UCG-005 and Prevotellaceae_UCG-004) were significantly enriched in faeces in comparison to milk and blood, except for Anaplasma which was greatly enriched in blood and was in turn the largest microbial genus in the entire analysis. This study provides insights into the microbial community composition of the sampled body sites and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the community of Waaihoek in KwaZulu-Natal, Republic of South Africa pertaining to their unsanitary practices associated with the use of cattle by-products.

The Effects of Non-Fiber Carbohydrate Content and Forage Type on Rumen Microbiome of Dairy Cows

Simple Summary

For sustainable development in the dairy industry, crop by-products play an important role, especially in areas that lack pasture and are not suitable for intensive cereal-adapted production (i.e., diets containing high amounts of cereal grains). However, feeding crop by-products usually lowers milk production in dairy cows due to their poor nutrient quality. In a previous study, we have demonstrated that non-fiber carbohydrate content (NFC) is a major limiting factor for the utilization of diets based on corn stover (CS). Although the higher abundance of easily fermentable energy in NFC and forage type can influence the synthesis of VFAs and MCP in the rumen and higher NFC content or high quality forages normally have a positive influence on the lactation performance of dairy cows, the underlying microbial mechanisms and potential effects on milk production are under-investigated to date. Here, we examined microbial composition and predicted the metabolism from cows fed CS-based diets with either high levels of NFC (H-NFC), or low levels of NFC (L-NFC). Control cows were fed an alfalfa-based diet (AH). Our results show that, supplementation of the CS-based diet with additional NFC increased amino acid biosynthesis in rumen microbiota in dairy cattle, and thus resulted in better nitrogen conversion. However, lower levels of fibrolytic capacity may limit dry matter intake of cows fed H-NFC and may prevent increased milk yield.

Abstract

The main objective of our current study was evaluating the effects of NFC supplementation and forage type on rumen microbiota and metabolism, by comparing microbial structures and composition among samples collected from cows fed AH (alfalfa-based diet), H-NFC (CS-based diet with high NFC) and L-NFC (CS-based diet with low NFC) diets. Our results show that microbial communities were structurally different but functionally similar among groups. When compared with L-HFC, NFC increased the population of Treponema, Ruminobacter, Selenomonas and Succinimonas that were negatively correlated with ruminal NH3-N, and urea nitrogen in blood, milk and urine, as well as significantly increasing the number of genes involved in amino acid biosynthesis. However, when compared to the AH group, H-NFC showed a higher abundance of bacteria relating to starch degradation and lactate production, but a lower abundance of bacteria utilizing pectin and other soluble fibers. This may lead to a slower proliferation of lignocellulose bacteria, such as Ruminococcus, Marvinbryantia and Syntrophococcus. Lower fibrolytic capacity in the rumen may reduce rumen rotation rate and may limit dry matter intake and milk yield in cows fed H-NFC. The enzyme activity assays further confirmed that cellulase and xylanase activity in AH were significantly higher than H-NFC. In addition, the lower cobalt content in Gramineae plants compared to legumes, might have led to the significantly down-regulated microbial genes involved in vitamin B12 biosynthesis in H-NFC compared to AH. A lower dietary supply with vitamin B12 may restrict the synthesis of milk lactose, one of the key factors influencing milk yield. In conclusion, supplementation of a CS-based diet with additional NFC was beneficial for nitrogen conversion by increasing the activity of amino acid biosynthesis in rumen microbiota in dairy cattle. However, lower levels of fibrolytic capacity may limit dry matter intake of cows fed H-NFC and may prevent increased milk yield.

Flavonoid-Modifying Capabilities of the Human Gut Microbiome-An In Silico Study

Flavonoids are a major group of dietary plant polyphenols and have a positive health impact, but their modification and degradation in the human gut is still widely unknown. Due to the rise of metagenome data of the human gut microbiome and the assembly of hundreds of thousands of bacterial metagenome-assembled genomes (MAGs), large-scale screening for potential flavonoid-modifying enzymes of human gut bacteria is now feasible. With sequences of characterized flavonoid-transforming enzymes as queries, the Unified Human Gastrointestinal Protein catalog was analyzed and genes encoding putative flavonoid-modifying enzymes were quantified. The results revealed that flavonoid-modifying enzymes are often encoded in gut bacteria hitherto not considered to modify flavonoids. The enzymes for the physiologically important daidzein-to-equol conversion, well studied in Slackiaisoflavoniconvertens, were encoded only to a minor extent in Slackia MAGs, but were more abundant in Adlercreutzia equolifaciens and an uncharacterized Eggerthellaceae species. In addition, enzymes with a sequence identity of about 35% were encoded in highly abundant MAGs of uncultivated Collinsella species, which suggests a hitherto uncharacterized daidzein-to-equol potential in these bacteria. Of all potential flavonoid modification steps, O-deglycosylation (including derhamnosylation) was by far the most abundant in this analysis. In contrast, enzymes putatively involved in C-deglycosylation were detected less often in human gut bacteria and mainly found in Agathobacter faecis (formerly Roseburia faecis). Homologs to phloretin hydrolase, flavanonol/flavanone-cleaving reductase and flavone reductase were of intermediate abundance (several hundred MAGs) and mainly prevalent in Flavonifractor plautii. This first comprehensive insight into the black box of flavonoid modification in the human gut highlights many hitherto overlooked and uncultured bacterial genera and species as potential key organisms in flavonoid modification. This could lead to a significant contribution to future biochemical-microbiological investigations on gut bacterial flavonoid transformation. In addition, our results are important for individual nutritional recommendations and for biotechnological applications that rely on novel enzymes catalyzing potentially useful flavonoid modification reactions.

Reanalysis of the Mars500 experiment reveals common gut microbiome alterations in astronauts induced by long-duration confinement

Maintaining astronaut health throughout long-duration spaceflight is essential to the feasibility of a manned mission to Mars. The ground-based Mars500 experiment investigated long-duration health by isolating six astronauts for 520 days, the longest controlled human confinement study conducted to date. After 520 days, astronauts had uniform strength and lean body mass losses, and increased fasting plasma glucose, calprotectin, and neutrophil levels characteristic of intestinal inflammation but previous analyses revealed no common significant changes in gut microbiota. This study reanalysed data from early (days 7–45) and late (days 420–520) faecal samples and identified 408 exact sequence variants (ESVs), including 213 shared by all astronauts. Thirty-two ESVs were significantly differentially abundant over time, including depletion of keystone resistant starch degrading, anti-inflammatory and insulin sensitivity-associated species, such as Faecalibacterium prausnitzii, Ruminococcus bromii, Blautia luti, Anaerostipes hadrus, Roseburia faecis, and Lactobacillus rogosae, and enrichment of yet-to-be-cultured bacteria. Additionally, the extraordinary experimental confinement allowed observation of microbiota potentially shared between astronauts and their habitat. Forty-nine species were shared, representing 49% and 12% of the human and environmental microbiome diversity, respectively. These findings reveal the microbiota which significantly altered in relative abundance throughout confinement, including species known to influence inflammation and host glucose homeostasis consistent with astronaut symptoms. Identification of microbiome alterations after 520 days of isolation represents a missing piece connecting Mars500 astronaut physiological studies. Knowledge of the impact of long-term confinement upon the human microbiome helps to improve our understanding of how humans interact with their habitats and is a valuable step forward towards enabling long-duration spaceflight.

Communal living: glycan utilization by the human gut microbiota

Our lower gastrointestinal tract plays host to a vast consortium of microbes, known as the human gut microbiota (HGM). The HGM thrives on a complex and diverse range of glycan structures from both dietary and host sources, the breakdown of which requires the concerted action of cohorts of carbohydrate-active enzymes (CAZymes), carbohydrate-binding proteins, and transporters. The glycan utilization profile of individual taxa, whether 'specialist' or 'generalist', is dictated by the number and functional diversity of these glycan utilization systems. Furthermore, taxa in the HGM may either compete or cooperate in glycan deconstruction, thereby creating a complex ecological web spanning diverse nutrient niches. As a result, our diet plays a central role in shaping the composition of the HGM. This review presents an overview of our current understanding of glycan utilization by the HGM on three levels: (i) molecular mechanisms of individual glycan deconstruction and uptake by key bacteria, (ii) glycan-mediated microbial interactions, and (iii) community-scale effects of dietary changes. Despite significant recent advancements, there remains much to be discovered regarding complex glycan metabolism in the HGM and its potential to affect positive health outcomes.

The names Hungateiclostridium Zhang et al. 2018, Hungateiclostridium thermocellum (Viljoen et al. 1926) Zhang et al. 2018, Hungateiclostridium cellulolyticum (Patel et al. 1980) Zhang et al. 2018, Hungateiclostridium aldrichii (Yang et al. 1990) Zhang et al. 2018, Hungateiclostridium alkalicellulosi (Zhilina et al. 2006) Zhang et al. 2018, Hungateiclostridium clariflavum (Shiratori et al. 2009) Zhang et al. 2018, Hungateiclostridium straminisolvens (Kato et al. 2004) Zhang et al. 2018 and Hungateiclostridium saccincola (Koeck et al. 2016) Zhang et al. 2018 contravene Rule 51b of the International Code of Nomenclature of Prokaryotes and require replacement names in the genus Acetivibrio Patel et al. 1980

A recent publication has created the genus name HungateiclostridiumZhang et al. 2018 and the new combinations Hungateiclostridium cellulolyticum (Patel et al. 1980) Zhang et al. 2018, Hungateiclostridium aldrichii (Yang et al. 1990.) Zhang et al. 2018, Hungateiclostridium alkalicellulosi (Zhilina et al. 2006) Zhang et al. 2018, Hungateiclostridium clariflavum (Shiratori et al. 2009) Zhang et al. 2018, Hungateiclostridium straminisolvens (Kato et al. 2004) Zhang et al. 2018 and Hungateiclostridium saccincola (Koeck et al. 2016) Zhang et al. 2018 for names at the rank of species that were previously either included in the genus ClostridiumPrazmowski 1880, Acetivibrio Patel et al. 1980 or HerbivoraxKoeck et al. 2016. Rules 23a, 38, 39b, 41a, 42 and 44 have not been followed and an illegitimate name at the rank of genus or illegitimate combinations at the rank of species as defined in Rule 51b(1) and (2) have been created. Another aspect is recognising the fact that an instance of heterotypic synonym has been created between Acetivibrio Patel et al. 1980, HerbivoraxKoeck et al. 2016 and HungateiclostridiumZhang et al. 2018, where the earliest validly published genus name is Acetivibrio Patel et al. 1980, of which the nomenclatural type is Acetivibrio cellulolyticus Patel et al. 1980. It follows from Rules 23a, 38, 39a, 39b, 41a, 42 and 44 that the genus name to be used is Acetivibrio Patel et al. 1980, with new combinations in that genus replacing those published in the genus HungateiclostridiumZhang et al. 2018, which together with the genus name are illegitimate according to Rule 51b of the International Code of Nomenclature of Prokaryotes. Additional issues are also addressed with regards to the names Pseudoclostridium thermosuccinogenes (Drent et al. 1995) Zhang et al. 2018, PseudoclostridiumZhang et al. 2018 OscillospiraceaePeshkoff 1940 (Approved Lists 1980), RuminococcaceaeRainey 2010, Eubacteriales Buchanan 1917 (Approved Lists 1980) and ClostridialesPrévot 1953 (Approved Lists 1980).

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.

An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017

Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.