Longitudinal Study of the Effects of Flammulina velutipes Stipe Wastes on the Cecal Microbiota of Laying Hens

Jiali Wei; Huanwei Xiao; Yingbo Wei; Ivan Stève Nguepi Tsopmejio; Chang Sun; Haoyuan Wu; Zhouyu Jin; Hui Song

doi:10.1128/msystems.00835-22

. 2022 Dec 13;8(1):e00835-22. doi: 10.1128/msystems.00835-22

Longitudinal Study of the Effects of Flammulina velutipes Stipe Wastes on the Cecal Microbiota of Laying Hens

Jiali Wei ^a, Huanwei Xiao ^a, Yingbo Wei ^a, Ivan Stève Nguepi Tsopmejio ^a, Chang Sun ^a, Haoyuan Wu ^a, Zhouyu Jin ^a, Hui Song ^a,^b,^c,^✉

Editor: Suzanne Lynn Ishaq^d

Reviewed by: Yunhe Xu^e

PMCID: PMC9948703 PMID: 36511708

ABSTRACT

Because antibiotics have been phased out of use in poultry feed, measures to improve intestinal health have been sought. Dietary fiber may be beneficial to intestinal health by modulating gut microbial composition, but the exact changes it induces remain unclear. In this study, we evaluated the effect of Flammulina velutipes stipe wastes (FVW) on the cecal microbiotas of laying chickens at ages spanning birth to 490 days. Using clonal sequencing and 16S rRNA high-throughput sequencing, we showed that FVW improved the microbial diversity when they under fluctuated. The evolvement of the microbiota enhanced the physiological development of laying hens. Supplementation of FVW enriched the relative abundance of Sutterella, Ruminiclostridium, Synergistes, Anaerostipes, and Rikenellaceae, strengthened the positive connection between Firmicutes and Bacteroidetes, and increased the concentration of short-chain fatty acids (SCFAs) in early life. FVW maintains gut microbiota homeostasis by regulating Th1, Th2, and Th17 balance and secretory IgA (S-IgA) level. In conclusion, we showed that FVW induces microbial changes that are potentially beneficial for intestinal immunity.

IMPORTANCE Dietary fiber is popularly used in poultry farming to improve host health and metabolism. Microbial composition is known to be influenced by dietary fiber use, although the exact FVW-induced changes remain unclear. This study provided a first comparison of the effects of FVW and the most commonly used antibiotic growth promoter (flavomycin) on the cecal microbiotas of laying hens from birth to 490 days of age. We found that supplementation with FVW altered cecal microbial composition, thereby affecting the correlation network between members of the microbiota, and subsequently affecting the intestinal immune homeostasis.

KEYWORDS: dietary fiber, Flammulina velutipes, flavomycin, microbiota, laying hens

INTRODUCTION

The microbial communities inhabiting the gastrointestinal tract play an important role in nutrient digestion, energy utilization, and immune system regulation (1). These regulatory effects are mediated by the complex microbial interactions and metabolites generated by the members of the microbial community (2, 3). The intestinal microbiota possesses genes encoding active enzymes of carbohydrates, which can decompose dietary fiber which is not digested by the host and produce short-chain fatty acids (SCFAs), mainly acetate, propionate, and butyrate (4). SCFAs affect host energy utilization. First, SCFAs, especially butyrate, are the energy substrates for colonic cells (5), and second, propionate is a substrate for the gluconeogenesis that can induce intestinal gluconeogenesis, signaling through the central nervous system to protect the host from diet-induced obesity and associated glucose intolerance (6). Third, acetate may help to improve metabolic health by increasing energy expenditure through whole-body fat browning (7). SCFAs can also act as signaling molecules to regulate host immunity. The combination of propionate and butyrate effectively inhibits the lipopolysaccharide (LPS)-induced inflammatory response of regulatory T cells (Treg cells) and reduces the production of inflammatory cytokines such as interleukin 6 (IL-6) and IL-12 (8).

A healthy gut microbial state, characterized by a high diversity of microorganisms, improves the functional diversity as well as microbe-microbe and host-microbe interactions. It is also called an equilibrium state or steady state (9, 10). In contrast, microbial imbalance can induce inflammatory responses mediated by Th1, Th2, and Th17 cells (11, 12). The Th cells activated by intestinal epithelial cells induce B cells to produce and secrete antibodies on the surface of the intestinal mucosa, mainly secreted immunoglobulin A (IgA). The secretory immunoglobulin A (S-IgA) may promote the retention of beneficial members of the intestinal flora and the removal of opportunistic pathogens through different binding methods (13).

Antibiotic growth promoters (AGPs) have played a decisive role in animal husbandry for more than half a century (14). Among them, flavomycin (synonyms: bambermycin, monomycin, flavophospholipol) is a typical glycolipid phosphate antibiotic that acts on Gram-positive bacteria and mainly plays a role in promoting the growth performance of chickens (15, 16). However, the overuse of antibiotics has led to a rise in antimicrobial resistance. In response to this threat to public health, the European Union introduced a ban on the use of antibiotics as growth promoters in 2006 (17). Therefore, this crutch of the poultry industry must be replaced.

In recent years, a growing number of scientific studies have shown positive effects of dietary fiber on chicken health and productivity (18 –20). Feeding experiments were mainly carried out with insoluble fiber sources that arise as by-products during industrial production, such as oat hulls, sunflower hulls, soybean hulls, wheat bran, and wood shavings (21). Flammulina velutipes is one of the most popular edible fungi and is rich in biological nutrients (carbohydrate, dietary fiber, glycoproteins, polyphenols, etc.) (22, 23). The annual output of F. velutipes in China exceeded 2.5 million tons from 2013 to 2019 (24); meanwhile, large amounts of the by-product F. velutipes stipe wastes (FVW) have also been produced. Previous studies have found that dietary FVW supplementation has no reverse regulation effect on the growth of laying hens but can increase antibody titers, enhance immune responses, promote calcium deposition in eggshells, and improve antioxidant capacity in serum and egg yolk (25 –28).

The phylogenetic composition of the microbiota commonly found in different gut segments of broilers has been well characterized (29), whereas the literature describing this characteristic of laying hens is very limited. The long-term diet is strongly associated with the composition, activity, and dynamics of the gut microbiome, while short-term dietary changes are often not sufficient to elicit major changes in the ecosystem (30, 31). Laying hens live up to approximately 70 weeks before their laying rate decreases to about 65%. The previous studies reported the influence of microbial changes on outcome at different ages, preventing interstudy comparisons (32 –34). Therefore, this study was designed to estimate the effects of FVW or flavomycin (FLA) on the cecal microbiota at different feeding stages by clonal sequencing and 16S rRNA gene analysis. The final purpose was to elucidate the regulatory effects of FVW on the microbiotas of laying hens. This study will provide a theoretical basis for using FVW as a prebiotic to maintain intestinal health of laying hens.

RESULTS

The diversity of the cecal microbiota in laying hens evolves with age and diet.

The impact of FVW on the cecal microbiota was assessed over a long study period, 490 days, with 450 laying hens divided into five diet supplementation groups (Fig. 1). Ninety chickens were randomly divided into 3 replicates in each group and received 5 ppm FLA, low (2%) FVW (LFVW), medium (4%) FVW (MFVW), high (6%) FVW (HFVW), or basic (unsupplemented) diet (BD). Nine chickens in each group were sacrificed and cecal contents were collected at day 7 (prestarter), day 28 (starter), day 70 (grower), day 112 (developer), and day 490 (finisher) to assess longitudinal microbial development.

FIG 1 — Overview of feeding and sampling strategies. A total of 450 1-day-old ISA laying hens were randomly divided into five groups, as shown. Each group was divided into 3 replicates with 30 chickens per replicate. Feed for laying hens was formulated for prestarter (age 0 to 7 days), starter (age 8 to 28 days), grower (age 29 to 70 days), developer (age 71 to 112 days), and finisher (age 113 to 490 days) production phases. Samples were collected at the end of each phase, as indicated by time points marked with orange circles.

To investigate the evolution of the cecum microbiota over time, alpha diversities were compared at the end of the five phases (prestarter, starter, grower, developer, and finisher). In general, the richness, diversity, and evenness gradually increased over time, while the richness and diversity were lower in the starter phase (P < 0.01), and this might be due to the cascading perturbations of external factors (Fig. 2A to C). In the starter phase, richness and diversity were higher in the FVW and FLA groups than in the BD group (P < 0.01) (Fig. 2D and E; also, see Fig. S1A to C in the supplemental material). In the grower phase, the richness was higher in the LFVW and MFVW groups than the BD group (P < 0.05) (Fig. 2D). In the developer phase, the evenness was lower in the HFVW group than the FLA group (P < 0.05) (Fig. 2F). This might indicate that FVW could improve the diversity of the gut microbiota when there are fluctuations in the gut microbiota development.

FIG 2 — The distribution of alpha diversity represents changes in the diversity of gut microbiota in the cecum of laying hens by age and supplementation. (A to C) Richness (A), Shannon-Wiener (B), and evenness (C) indices indicate that the overall diversity increases with phases. (D to F) Richness (D), Shannon-Wiener (E), and evenness (F) indices indicate that the relative diversity changes by supplementation. There were statistically significant differences in community structure among different supplemental groups. P values were adjusted for multiple testing using one-way ANOVA. *, *P <* 0.05; **, *P <* 0.01; ***, *P <* 0.001; ****, *P <* 0.0001.

FIG S1

Diversity of cecal microbiota in laying hens in the finisher phase (16S high-throughput sequencing). (A) Sobs, richness index; (B) Shannon, diversity index; (C) Shannoneven, evenness index. (D) Differences in microbial composition were demonstrated using PCA of Bray-Curtis dissimilarity. Download FIG S1, TIF file, 0.9 MB^{(948.5KB, tif)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

The discriminant distribution between samples from different feeding phases were described by principal-component analysis (PCA). Analysis of similarities (ANOSIM) showed that flock development exerted a substantial influence on overall community variations (P = 0.0001) (Fig. 3A). In the starter, grower, and developer phases, samples from the MFVW and HFVW groups clustered separately from those of the BD and FLA groups (Fig. 3C to E), while in the finisher phase, the cecal microbiotas of laying hens tended to be homogenous (P = 0.1567) (Fig. 3F; Fig. S1D). Chickens receiving the BD and the FLA-supplemented diet harbored similar microbial profiles, as they clustered together in each of five phases (Fig. 3B to F). Thus, the increase in community diversity was accompanied by decreased heterogeneity of the cecal microbiota.

FIG 3 — Differences in microbial composition were demonstrated using PCA of Bray-Curtis dissimilarity in all phases (A) and in the prestarter (B), starter (C), grower (D), developer (E), and finisher (F) phases. Beta diversity relationships are summarized in two-dimensional scatterplots. Each point represents a sample, and distances between dots are representative of differences in microbiota compositions. There were statistically significant differences in community structure among different supplement groups (R > 0, *P <* 0.05).

Succession of dominant gut microbiotas in the cecum of laying hens.

The succession of dominant gut microbiotas in the cecum of laying hens was traced at the taxonomic levels of phylum, class, order, family, and genus (Fig. 4; Fig. S2). Firmicutes was the dominant phylum in the prestarter and starter phases, while Firmicutes, Bacteroidetes, and Proteobacteria were dominant in the last three phases (Fig. 4A). Clostridiales was the dominant order throughout the feeding phases of laying hens, with a relative abundance greater than 80% in the first two phases, while in the last three phases, Bacteroidales and Clostridiales were both dominant (Fig. 4B). At the family level, Ruminococcaceae were predominant in the prestarter phase. During the starter phase, Lachnospiraceae transitioned to the dominant family. During the grower phase, Bacteroidaceae replaced Lachnospiraceae as the dominant family, while the predominance of Bacteroidaceae was diluted by Eubacteriaceae and Pseudomonadaceae in developer phase. At the finisher phase, Prevotellaceae, Eubacteriaceae, Rikenellaceae, and Bacteroidaceae became the dominant families (Fig. 4C). At the genus level, Ruminococcus, Bariatricus, Intestinimonas, Pseudoflavonifractor, and Lachnoclostridium were predominant in the prestarter phase. Lachnoclostridium, Blautia, and Roseburia were dominant in the starter phase. Bacteroides, Ruminiclostridium, and Barnesiella were dominant in the grower phase, while Pseudoflavonifractor, Bacteroides, Eubacterium, and Acinetobacter were the most important in the developer phase. Finally, Alistipes, Eubacterium, and Prevotella were the dominant genera in the finisher phase (Fig. 4D). At the end of the feeding period (in the finisher phase), the linear discriminant analysis effect size (LEfSe) multilevel discriminant analysis of species differences indicated that compared to the BD group, the FLA group was differentially enriched in Ruminococcaceae, Desulfovibrio, Peptococcus, Enterorhabdus, and Faecalicoccus (Fig. 5A). In the LFVW group, Sutterella and Ruminiclostridium were differentially enriched (Fig. 5B), while Synergistes and Anaerostipes were enriched in the MFVW group (Fig. 5C) and Rikenellaceae and Synergistes in the HFVW group (Fig. 5D).

FIG 4 — Composition and succession of gut microbiota in laying hens. Stacked bar plots represent the diet-induced distortions in the main phylum (A), order (B), family (C), and genus (D). B, BD; F, FLA; L, LFVW; M, MFVW; H, HFVW.

FIG 5 — Shifts in taxa of the main cecal microbiomes of laying hens. LEfSe multilevel discriminant analysis of species differences in the finisher phase between (A) BD and FLA, (B) BD and LFVW, (C) BD and MFVW, and (D) BD and HFVW.

FIG S2

Composition and succession of taxa in the gut microbiota in laying hens. Stacked bar plots represent the diet-induced distortions in the main class. Download FIG S2, TIF file, 0.7 MB^{(766.2KB, tif)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

FVW supplementation altered the co-occurrence network of the cecal microbiota.

The pattern of interbacterial interactions among the cecal microbial communities was analyzed by constructing the co-occurrence network of each group (based on Spearman correlation). The metacommunity cooccurrence networks of the BD, FLA, LFVW, MFVW, and HFVW groups comprised, respectively, 159 edges, 154 edges, 143 edges, 159 edges, and 152 edges, representing 30 interactive genera (Fig. 6). In the FLA group, the largest numbers of positive relationships between Firmicutes and Firmicutes, Bacteroidetes, and Bacteroidetes and of negative relationships between Firmicutes and Bacteroidetes were found. Meanwhile, the fewest negative correlations between Firmicutes and Firmicutes, Bacteroidetes, and Bacteroidetes and positive correlations between Firmicutes and Bacteroidetes were also found (Fig. 6B). The long-term supplementation of FVW changed the interaction between members of the gut microbiota, as shown by the strengthening positive correlation between Firmicutes and Bacteroidetes and the weakening positive correlation between Firmicutes and Firmicutes. Among them, MFVW supplementation caused the most significant changes in microbial interactions (Fig. 6A to E). These results might indicate that the supplementation of fiber-rich FVW affects the composition of carbon sources available to microorganisms and then changes the energy utilization among the intestinal microorganisms.

FIG 6 — Spearman’s correlation network analyses showing genus-level interactions among cecal microbes. The different-color nodes represent the phyla of the detected genera. The style of the edge indicates positive (pink solid line) and negative (blue dotted line) correlation, and the line thickness shows the correlation strength. (A) BD, (B) FLA, (C) LFVW, (D) MFVW and (E) HFVW. Only significant correlations are shown (cutoff threshold, Spearman’s coefficient > 0.7 and P < 0.5).

FVW supplementation increased SCFA concentrations in the early life of laying hens.

The microbiota in the cecum ferments undigested carbohydrates by using its own glycohydrolytic activity to produce SCFAs (35). SCFAs play a role in regulating immunity by acting on epithelial and immune cells (36). Acetate, propionate, and butyrate were maintained at a stable level throughout the feeding phases of laying hens (Table 1). The FVW supplementation accelerated SCFA production in the early life (prestarter and starter phases) of laying hens, while FLA mainly promoted the production of SCFAs during the grower and developer phases (P < 0.05) (Table 1). In the prestarter phase, acetate levels were higher in the MFVW (9.05 ± 0.44 mmol/L) and HFVW (9.39 ± 0.33 mmol/L) groups than in the BD (7.26 ± 0.10 mmol/L) and FLA (6.62 ± 0.04 mmol/L) groups (P < 0.5). Broadly, the highest level of propionate was found in the LFVW group. In the starter phase, acetate, propionate, and butyrate were significantly increased in the FLA and FVW supplementation groups compared to the BD group (P < 0.05). In the grower and developer phases, the FLA group showed the highest concentration of acetate and butyrate, while the HFVW group showed the lowest concentration of SCFAs in general (P < 0.05). In the finisher phase, SCFAs were significantly reduced in the FLA and FVW groups (P < 0.05) (Table 1).

TABLE 1.

Effect of dietary supplementation of FVW on SCFA concentration in chickens

Phase	SCFAs	Concn (mmol/L) in chickens fed diet with^a:
Phase	SCFAs	BD	FLA	LFVW	MFVW	HFVW
Prestarter	Acetate	7.26 ± 0.10 b	6.62 ± 0.03 a	6.92 ± 0.11 ab	9.05 ± 0.44 c	9.39 ± 0.33 c
	Propionate	0.28 ± 0.01 c	0.25 ± 0.00 b	0.32 ± 0.01 d	0.25 ± 0.00 b	0.17 ± 0.03 a
	Butyrate	1.08 ± 0.03 e	1.01 ± 0.04 d	0.94 ± 0.02 c	0.89 ± 0.02 b	0.44 ± 0.00 a
	Total SCFAs	8.62 ± 0.11 b	7.88 ± 0.01 a	8.19 ± 0.11 a b	10.19 ± 0.45 c	9.99 ± 0.33 c

Starter	Acetate	5.32 ± 0.58 a	15.24 ± 1.74 c	10.88 ± 1.29 b	11.64 ± 1.29 b	13.16 ± 1.31 bc
	Propionate	0.42 ± 0.01 a	0.59 ± 0.03 b	0.37 ± 0.01 a	1.25 ± 0.05 c	0.57 ± 0.07 b
	Butyrate	0.57 ± 0.04 a	1.83 ± 0.07 b	1.70 ± 0.04 b	1.74 ± 0.14 b	1.84 ± 0.05 b
	Total SCFAs	6.31 ± 0.61 a	17.66 ± 1.74 c	12.95 ± 1.32 b	14.62 ± 1.40 b	15.57 ± 1.74 bc

Grower	Acetate	5.53 ± 0.25 b	8.21 ± 0.17 d	6.00 ± 0.21 c	5.11 ± 0.19 a	4.78 ± 0.13 a
	Propionate	1.13 ± 0.04 c	1.06 ± 0.11 c	0.55 ± 0.03 a	0.89 ± 0.05 b	0.53 ± 0.06 a
	Butyrate	0.68 ± 0.04 ab	0.98 ± 0.04 c	0.71 ± 0.04 b	0.61 ± 0.05 a	0.71 ± 0.03 b
	Total SCFAs	7.34 ± 0.31 c	10.25 ± 0.15 d	7.26 ± 0.17 c	6.61 ± 0.20 b	6.02 ± 0.15 a

Developer	Acetate	6.24 ± 0.03 d	7.41 ± 0.08 e	4.44 ± 0.28 c	3.78 ± 0.24 b	2.74 ± 0.06 a
	Propionate	1.51 ± 0.03 c	1.93 ± 0.14 d	0.91 ± 0.08 b	0.75 ± 0.02 a	0.67 ± 0.07 a
	Butyrate	0.46 ± 0.04 c	0.57 ± 0.04 d	0.5 ± 0.16 c	0.36 ± 0.04 b	0.28 ± 0.02 a
	Total SCFAs	8.22 ± 0.06 d	9.92 ± 0.12 e	5.85 ± 0.22 c	4.88 ± 0.19 b	3.69 ± 0.11 a

Finisher	Acetate	4.20 ± 0.45 c	2.45 ± 0.32 b	2.83 ± 0.41 b	2.34 ± 0.18 b	1.66 ± 0.02 a
	Propionate	1.63 ± 0.06 d	0.88 ± 0.04 b	1.06 ± 0.06 c	0.59 ± 0.04 a	0.52 ± 0.03 a
	Butyrate	0.71 ± 0.06 d	0.39 ± 0.01 b	0.55 ± 0.04 c	0.34 ± 0.02 b	0.24 ± 0.01 a
	Total SCFAs	6.54 ± 0.43 d	3.72 ± 0.34 b	4.43 ± 0.08 c	3.27 ± 0.17 b	2.42 ± 0.05 a

Open in a new tab

Values are means and standard deviations. Letters indicate significance (P < 0.05).

FVW regulated the homeostasis of intestinal mucosal immunity in laying hens.

The role of the microbiome is especially crucial in early life for the development of the immune system. A microbial imbalance could induce inflammatory responses mediated by Th1, Th2, and Th17 cells (12). Th1 and Th17 cells secrete proinflammatory cytokines, while Th2 cells secrete anti-inflammatory cytokines. The levels of the proinflammatory cytokines tumor necrosis factor alpha (TNF-α) and IL-6 were significantly reduced in the FVW groups compared with those in the BD and FLA groups during the prestarter and starter phases (P < 0.05) (Fig. S3A to D). IL-2 is known to promote the differentiation of the anti-inflammatory cytokine IL-10 (37). The level of IL-2 significantly increased in the FVW compared to the BD and FLA groups (P < 0.05) (Fig. S3G and H). The levels of the anti-inflammatory cytokine IL-4 significantly increased in the MFVW and HFVW groups (Fig. S3I). FVW supplementation significantly increased the levels of S-IgA in the small intestinal mucosa compared to the BD and FLA groups (P < 0.05) (Fig. S3M and N). The levels of IL-6 and IL-2 were significantly increased in the FLA group compared to the BD group (Fig. S3C and H). The other cytokines did not change significantly between groups (Fig. S3). Therefore, FVW could regulate the dynamic balance of intestinal mucosal immunity in laying hens, which might be beneficial for the homeostasis of the commensal microbiota.

FIG S3

Profile of cytokine levels in the small-intestinal mucosa. (A) TNF-α in the prestarter phase, (B) TNF-α in the starter phase, (C) IL-6 in the prestarter phase; (D) IL-6 in the starter phase; (E) IL-17 in the prestarter phase; (F) IL-17 in the starter phase; (G) IL-2 in the prestarter phase; (H) IL-2 in the starter phase; (I) IL-4 in the prestarter phase; (J) IL-4 in the starter phase; (K) IL-10 in the prestarter phase; (L) IL-10 in the starter phase; (M) S-IgA in the prestarter phase; (N) S-IgA in the starter phase. P values were adjusted for multiple testing using one-way ANOVA. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. Download FIG S3, TIF file, 1.3 MB^{(1.3MB, tif)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

DISCUSSION

The gut microbiota of laying hens plays a crucial role in host health and development. Dietary fiber could act as a prebiotic to regulate the intestinal health of chickens (38), but the effects of long-term dietary interventions on the gut microbiotas of laying hens were largely unknown. Therefore, our study aimed to evaluate the effects of fiber-rich Flammulina velutipes stipe waste (FVW) on the microbiota of laying hens, using FLA (flavomycin), an antibiotic growth promoter commonly used in laying hens, as a reference for 70 weeks. FVW induced beneficial changes in the cecal microbiota of laying hens. It changed the interaction network between bacteria and regulated the homeostasis of intestinal mucosal immunity. These results demonstrate that the long-term feeding of fiber-rich FVW may serve as a potential prebiotic alternative to the use of antibiotic growth promoters.

FVW increased the diversity of the gut microbiota in laying hens during starter phase. A higher diversity of gut microbiota is associated with a healthier physiological state (39). The factors influencing gut microbiota diversity include host factors and environmental factors, such as age and diet (40, 41). Previous studies reported that dietary fiber supplementation has no significant effect on the gut microbiota diversity of laying hens during the grower and developer phases (9 to 20 weeks of age) and the finisher phase (89 weeks of age) (42, 43). Furthermore, studies on the gut microbiota in the early life of laying hens are very limited. These results confirmed the conjecture of this study that the starter period is the key period for the development of the gut microbiota in laying hens and that a diet with FVW as a source of fiber could increase the diversity of the gut microbiota during this period. Supplementation of almond hulls (rich in insoluble dietary fiber) had no effect on broiler cecal microbiota diversity (44), while alfalfa (rich in fiber) increased intestinal microbiota diversity (45). The different results may be due to the fact that the fiber sources in FVW are mainly hemicellulose and cellulose. Previous studies have shown that antibiotic growth promoters (flavomycin and virginiamycin) could increase the richness of the gut microbiota in broiler chickens but have no significant effect on the diversity (46), which is consistent with the results of this study showing that the subtherapeutic dose of flavomycin did not destroy the diversity of the gut microbiota. In this study, the structure of the gut microbiota showed convergence and stability with increasing age, which is in agreement with the previous results obtained with laying hens (47). However, the heterogeneity of the gut microbiota structure in broiler chickens increased over time (48). This contrasting result suggests that the farming duration and chicken type lead to differences in the structural development of the gut microbiota. Our results emphasized that the starter phase (0 to 28 days) may the optimal time for FVW to intervene and influence the microbiome.

Firmicutes was the absolute dominant phylum during the first 4 weeks of the laying hens’ life, in response to the high-protein feed composition during the brood stage of bone and muscle development. Bacteroidetes began to become the dominant phylum after the grower phase of laying hens in response to the increase in dietary fiber. The long-term dietary intervention led to a change in gut microbiota intestinal type (31). An increase in the abundance of Sutterella, Synergistes, Anaerostipes, Ruminiclostridium, and Rikenellaceae in the gut caused by long-term addition of FVW was also observed in this study. Sutterella is an obligately anaerobic, Gram-negative bacterium (49), and there is a negative correlation between the presence or abundance of Sutterella and the host inflammatory cytokine response (50, 51). Synergistes is related to reduce gastrointestinal inflammation and enhances immune function (52). Anaerostipes is a butyrate producer, which could convert lactate and acetic acid and sugar to butyrate (53 –56). Ruminiclostridium is an anaerobic Gram-positive cellulolytic bacterium that produces a variety of carbohydrate-active enzymes (CAZymes) and catabolizes xyloglucan into glucose, xylose, galactose, and cellobiose (57). It includes extracellular multienzyme complexes known as fibrosomes with different specificities to enhance the degradation of cellulosic biomass (58). FLA causes enrichment of Ruminococcaceae, Desulfovibrio, Peptococcus, Enterorhabdus, and Faecalicoccus. Ruminococcaceae is a recognized SCFA-producing bacterium (59). Desulfovibrio is a Gram-negative anaerobe belonging to the sulfate reducing group (60). Sulfate-reducing bacteria could use organic compounds (lactate, propionate, and butyrate) as sources of energy and carbon (61, 62). The expansion of Desulfovibrio has been reported to be associated with inflammatory bowel disease, including ulcerative colitis (63 –65). Peptococcus was found to be strongly positively correlated with the body weight (BW) and average daily gain (ADG) in pig culture experiments (66). In an immune experiment with mice, Peptococcus was found to be positively correlated with LPS, d-lactic acid, and TNF-α (67). Enterorhabdus is an obesity-promoting bacterium associated with diabetes and other metabolic diseases, while the overgrowth of Enterorhabdus is also a sign of ecological imbalance after antibiotic use (68 –70). The enrichment of Faecalicoccus is usually associated with intestinal inflammation, including ulcerative colitis and Crohn’s disease (71). These results are consistent with previous findings that dietary-fiber-rich by-products could modulate the composition of the cecal microbiota of chickens (72 –74).

In addition, FVW increased the positive-relationship cluster between Firmicutes and Bacteroidetes. Previous studies have shown a strong negative relationship between Bacteroidales and Clostridiales in the cecum of chickens fed a basic diet (75). Firmicutes and Bacteroidetes represented most of the anaerobic fermentative bacteria (76), which may present nutritional competition for fermentation substrates in the cecum (77). The gut microbiome typically relies on carbohydrates as its energy source, and the gut microbes that use the same energy source occupy the same niche and form a competitive symbiotic relationship (78, 79). FVW might provide abundant dietary fiber for the gut microbiota, thereby changing the interaction between members of the microbiota (from competitive symbiosis to mutualistic symbiosis). In contrast with previous studies, this study supports the intervention effect of dietary fiber supplementations on the microbe-microbe interaction (19, 80, 81).

Subsequently, FVW increased acetate and propionate, but not butyrate. Intestinal bacteria ferment dietary fiber to produce short-chain fatty acids, which play an important role in immune regulation (82). The result is consistent with the previous report showing that insoluble dietary fiber can increase the content of acetate and propionate in the cecum (83). Bacteroidetes could ferment dietary fiber to produce acetate, isovalerate, and succinate, of which succinate is the raw material required for propionate production (84). Acetate strengthens the barrier function by mediating the signaling pathways that enable B cells and goblet cells to secrete mucins and IgA (85). Propionate could promote the development of Treg cells and reduce the expansion of inflammatory Th17 cells (86). Long-term propionate delivery in the colon improved glucose homeostasis, along with the suppression of systemic imperial inflammation (87). These results suggest that FVW may regulate the intestinal immunity by increasing acetate and propionate.

The intestinal immune system must maintain a delicate balance between tolerance of commensal microbiota and immunity to pathogens, maintaining low responsiveness to the commensal microbiota at steady state (88). Previous studies have shown that supplementation with dietary fiber could reduce levels of the proinflammatory factors TNF-α, IL-1β, and IL-6 (89). In this study, FVW decreased the levels of the proinflammatory cytokines TNF-α and IL-6 and increased the levels of the anti-inflammatory cytokine IL-4. Additionally, the biomarker of the intestinal mucosa immune response is the production of secretory immunoglobulin A (S-IgA). It is the most prominent antibody present in mucosal surfaces and protects the intestinal mucosa against the invasion of enteric toxins and pathogenic microorganisms (13, 90). In this study, FVW increased the levels of S-IgA in the small-intestinal mucosa. Similar to our results, dietary fiber (wheat bran and sugar beet pulp) and prebiotics (xylo-oligosaccharides and mannooligosaccharides) increased the amount of S-IgA in the small intestine (91 –93). The above results further proved that FVW has the potential of prebiotics to regulate the host immunity microbes in steady state.

In conclusion, we found that FVW, which is rich in dietary fiber, altered the interaction between members of the gut microbiota, regulated the balance between gut microbiota and host immunity, and kept the gut microbiota in a healthy and stable state. Against the background of an antibiotic-free culture, this study provides data supporting the development and application of Flammulina velutipes stipe wastes as potential prebiotics for laying hens. This study was a small-scale farming experiment under laboratory conditions, which could not fully simulate the factory feeding conditions and environmental stress caused by a large breeding base. Therefore, focusing on the interaction network and the competition and cooperation between members of the gut microbiota will be the next direction of our research.

MATERIALS AND METHODS

Experimental design and sample collection.

A 490-day study assessing the impact of Flammulina velutipes stipe wastes (FVW) on the cecal microbiota of the laying chicken was performed in Animal Feeding Room, Jilin Agricultural University, Changchun, China. FVW were provided by China Changchun Xuerong Biotechnology Co., Ltd. The collected FVW were naturally dried and then transferred to a feed factory for further use (Jilin Hanhong Animal Husbandry Co., Ltd.). A total of 450 ISA brown laying chicks, purchased from a commercial hatchery, were randomly divided into 5 groups (3 replicates/group, 30 chickens/replicate): BD (basic diet), FLA (basic diet supplemented with 5 ppm flavomycin), LFVW (basic diet supplemented with 2% FVW), MFVW (basic diet supplemented with 4% FVW), and HFVW (basic diet supplemented with 6% FVW). The different groups were fed ad libitum with starter feed from 1 to 28 days, grower from 29 to 70 days, developer from 71 to 112 days, and finisher from 113 to 490 days (Fig. 1). The nutritional components of Flammulina velutipes stipe wastes are shown in Table S1. All feedings were applied according to the NRC-1994 norms and the principle of equal energy and equal nitrogen (Table 2 and Tables S2 to S5).

TABLE 2.

Basal composition and nutrient levels of chicken diet

Ingredient or component	% in diet at phase
Ingredient or component	Starter	Grower	Developer	Finisher
Composition
Maize corn	63.14	67.25	67.50	55.70
Soybean oil	0.60	1.00	0.00	2.80
Soybean meal	32.20	27.50	25.50	28.20
Lysine	0.20	0.20	0.20	0.20
Methionine	0.25	0.20	0.25	0.25
Dicalcium	2.20	2.30	3.00	3.60
Limestone	1.00	1.00	3.10	8.80
Common salt	0.21	0.35	0.25	0.25
Vitamins and minerals^a	0.20	0.20	0.20	0.20
Calculated nutrition level^b
DM	90.65	90.50	91.34	91.12
ME (MJ/kg)	12.05	12.21	11.69	11.70
CP	20.02	18.25	16.87	17.00
Ca	0.99	1.00	1.11	4.11
P	0.50	0.51	0.58	0.72
EE	3.41	0.39	0.29	0.52
CF	2.91	2.70	2.58	2.56
Lys	1.17	1.05	1.00	1.05
Methionine	0.53	0.46	0.50	0.50
Cystine	0.32	0.30	0.29	0.28

Open in a new tab

The premix provided is as follows (per kilogram of feed): vitamin A, 4,500 IU; vitamin D3, 1,200 IU; dl-α-tocopheryl acetate, 2,500 IU; vitamin B₁, 5,000 mg; vitamin B₂, 20,000 mg; vitamin K, 10,000 mg; niacin, 45,000 mg; pantothenic acid, 35,000 mg; biotin, 1,500 mg; folic acid, 3,000 mg; vitamin B₁₂, 40 mg; zinc, 45 mg; manganese, 50 mg; iron, 30 mg; copper, 4 mg; cobalt, 100 μg; iodine, 1 mg; selenium, 100 μg.

DM, dry matter; ME, metabolizable energy; CP, crude protein; Ca, calcium; P, phosphorus; EE, ether extract; CF, crude fiber.

TABLE S1

Nutrients of Flammulina velutipes stipe waste (air-dried basis, percent). Download Table S1, DOCX file, 0.02 MB^{(19.8KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

TABLE S2

Starter phase (0 to 28 days) composition and nutrient levels of diets (air-dried basis, percent). Download Table S2, DOCX file, 0.02 MB^{(21.3KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

The size of the brooding cage was 60 cm by 40 cm by 50 cm (length, width, and height, respectively), and there were 14 chickens per cage from 1 to 56 days and 7 chickens per cage from 57 to 112 days. At 112 days, the laying hens were moved to a laying cage (100 cm by 60 cm by 50 cm [length, width, and height, respectively]), with 3 chickens per cage. No veterinary treatment was required for the duration of the experiment.

Nine chickens per supplementation group were sacrificed at 5 defined time points: day 7 (prestarter), day 28 (starter), day 70 (grower), day 112 (developer), and day 490 (finisher). Intestinal and cecal samples were collected in College of Life Science Building, Jilin Agricultural University. Samples were quickly flash-frozen in liquid nitrogen and stored at −80°C until further processing.

DNA extraction.

The microbial DNA was extracted from digesta in ceca using the EZNA soil kit (Omega Bio-Tek, USA) according to the manufacturer’s protocol. The final DNA concentration and purification were determined with a NanoDrop 2000 instrument, and DNA quality was detected by 1% agarose gel electrophoresis.

PCR-DGGE and clonal sequencing.

The V3 hypervariable regions of the bacterial 16S rRNA gene were amplified with the primers F338-GC (5′-CGCCCGCCGCGCGCGGGGGGGCGGGGCGGGGGCAGGGGGGCCTCGGAGGCAGCAG-3′) and R518 (5′-ATTACCGCGGCTGCTGG-3′) with a thermocycler PCR system (MG25+; Thermo Scientific, China). The PCRs were conducted using the following program: 95°C predenaturation for 5 min, 30 cycles (95°C denaturation for 1 min, annealing at 60°C for 1 min, and extension at 72°C for 1 min), with a final extension at 72°C for 5 min. The PCRs were performed in triplicate using a 25-μL mixture containing 12.5 μL premix Taq mix, 10 μL sterilized ultrapure water, 0.5 μL forward primer, 0.5 μL reverse primer, and 1.5 μL of template DNA. A 230-bp DNA fragment was obtained and further analyzed by denaturing gradient gel electrophoresis (DGGE) with a denaturant gradient of 40% to 65% and a concentration of polyacrylamide gel of 8%. The gel was cut to recover clear consensus and specific bands in the DGGE map. The reamplified DNA fragment (without GC clamp) was purified, linked to the pESI-T vector, and transformed into DH5α cells. The positive clones were screened and sequenced at Sangon Biotech (Shanghai, China) Co., Ltd.

16S rRNA high-throughput sequencing.

The V3-V4 hypervariable regions of the bacterial 16S rRNA gene were amplified with primers F338 (5′-ACTCCTACGGGAGGCAGCAG-3′) and R806 (5′-GGACTACHVGGGTWTCTAAT-3′) with a thermocycler PCR system (GeneAmp 9700; ABI, USA). The PCRs were conducted using the following program: 95°C predenaturation for 3 min, 27 cycles of 95°C denaturation for 30 s, annealing at 55°C for 30 s, and extension at 72°C for 30 s, and a final extension at 72°C for 10 min. The PCRs were performed in triplicate 20-μL mixtures containing 4 μL of 5× FastPfu buffer, 2 μL of a 2.5 mM concentration of deoxynucleoside triphosphates (dNTPs), 0.8 μL primer (5 μM), 0.4 μL FastPfu polymerase, and 10 ng of template DNA. The resulted PCR products were extracted from a 2% agarose gel, further purified by using the AxyPrep DNA gel extraction kit (Axygen Biosciences, USA), and quantified using a QuantiFluor-ST system (Promega, USA) according to the manufacturer’s protocol. Purified amplicons were pooled in equimolar amounts and paired-end sequenced (2 × 300 bp) on an Illumina MiSeq platform (Illumina, San Diego, CA, USA) according to the standard protocol by Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China).

Determination of SCFAs concentration.

The experimental conditions were as follows: the chromatographic column was a DB-FFAP capillary column (30 m by 250 μm by 0.25 μm), the inlet temperature was 220°C, the flame ionization detector (FID) temperature was 250°C, the column temperature heating program consisted of an initial temperature of 65°C and then an increase to 190°C at a 20°C/min heating rate, the split ratio was 25:1, and gas flow rates were 25 mL/min for carrier gas (N₂), 40 mL/min for H₂, and 400 mL/min for air. The levels of acetate, propionate, and butyrate were detected with an Agilent gas chromatograph 7890A (Agilent Technologies, USA). The standard solution (mixed standard) used was 60 mmol/L (3.60 g/L) of acetate, 50 mmol/L (3.72 g/L) of propionate, and 20 mmol/L (1.76 g/L) of butyrate.

Determination of cytokines in intestinal mucosa.

TNF-α, IL-6, IL-17, IL-2, IL-4, IL-10, and S-IgA in the intestinal mucosa were measured by using chicken-specific enzyme-linked immunosorbent assay (ELISA) quantitation kits (Lengton Bioscience Co. Ltd., Shang Hai, China) according to the instructions of the manufacturer.

Data analyses.

Quantity One v.4.6.2 was used to analyze the fingerprint of PCR-DGGE and the gray value of each band. For microbial diversity analysis, the richness index is the number of bands, the Shannon-Wiener index was calculated as −∑ [ln(ni/∑ni) × (ni/∑ni)] = −∑ [ln (ni/∑ni) × (ni/∑ni)] (where ni is the gray value of the band), and the evenness index was calculated as H/lnS (where H is the Shannon-Wiener index and S is the richness index). The differences in the microbiota community structures were evaluated by PCA based on Bray-Curtis dissimilarity values and performed with Canoco v.5. BLAST comparison was performed in GenBank at the NCBI website to obtain the corresponding biological classification information for the bands.

For processing of data sequencing, Raw-fastq files were demultiplexed, quality filtered with Trimmomatic, and merged by FLASH with the following criteria. (i) The reads were truncated at any site receiving an average quality score of <20 over a 50-bp sliding window. (ii) By allowing 2-nucleotide mismatches, primers were exactly matched with the removal of possessing ambiguous reads. (ii) Sequences with an overlap of more than 10 bp were mixed according to their overlap sequences. Operational taxonomic units (OTUs) were accumulated with a similarity cutoff value of 97% by using UPARSE (version 7.1 [http://drive5.com/uparse/]); chimeric sequences were elaborated and removed by using UCHIME. The 16S rRNA gene sequence taxonomy was examined by the RDP Classifier algorithm (http://rdp.cme.msu.edu/) against the SILVA 138 16S rRNA database using a confidence threshold of 70%. Networks were then constructed by using the method implemented in Cytoscape v.3.7.1.

All data are expressed as means and standard deviations (SD) as determined by SPSS v.25. The results were analyzed with one-way analysis of variance (ANOVA) and Duncan’s multiple-comparison test. The differences were considered statistically significant at a P value of <0.05. All box plots, stacked bar charts, and bar charts were drawn using GraphPad Prism v.8.

Ethical approval.

All procedures in this project were conducted within the ethical regulations and standards set and carried out by the Animal Care Review Committee of Jilin Agricultural University (ID: 2019-08-28-001).

Data availability.

Sequence data generated in this study have been made available at the Sequence Read Archive (SRA) on NCBI under project number PRJNA628749.

TABLE S3

Grower phase (29 to 70 days) composition and nutrient levels of diets (air-dried basis, percent). Download Table S3, DOCX file, 0.02 MB^{(21.3KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

TABLE S4

Developer phase (71 to 112 days) composition and nutrient levels of diets (air-dried basis, percent). Download Table S4, DOCX file, 0.02 MB^{(21.2KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

TABLE S5

Finisher phase (113 to 490 days) composition and nutrient levels of diets (air-dried basis, percent). Download Table S5, DOCX file, 0.02 MB^{(21.3KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

Supplementary Material

Reviewer comments

reviewer-comments.pdf^{(557.2KB, pdf)}

ACKNOWLEDGMENTS

We express sincere gratitude to the doctoral students, especially Shad Mahfuz and Shuyuan Wang, who provided unconditional help during the experiment.

We have no conflict of interest to declare.

This work was supported by Department of Science and Technology of Jilin Province (no. JJKH20190917KJ).

Contributor Information

Hui Song, Email: songhuisk@jlau.edu.cn.

Suzanne Lynn Ishaq, The University of Maine.

Yunhe Xu, Department of Animal Husbandry & Veterinary Medicine, Jinzhou Medical University, Jinzhou, China.

REFERENCES

1.Sommer F, Bäckhed F. 2013. The gut microbiota—masters of host development and physiology. Nat Rev Microbiol 11:227–238. doi: 10.1038/nrmicro2974. [DOI] [PubMed] [Google Scholar]
2.van der Hee B, Wells JM. 2021. Microbial regulation of host physiology by short-chain fatty acids. Trends Microbiol 29:700–712. doi: 10.1016/j.tim.2021.02.001. [DOI] [PubMed] [Google Scholar]
3.Cani PD, Van Hul M, Lefort C, Depommier C, Rastelli M, Everard A. 2019. Microbial regulation of organismal energy homeostasis. Nat Metab 1:34–46. doi: 10.1038/s42255-018-0017-4. [DOI] [PubMed] [Google Scholar]
4.Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. 2014. The Carbohydrate-Active Enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495. doi: 10.1093/nar/gkt1178. [DOI] [PMC free article] [PubMed] [Google Scholar]
5.Donohoe DR, Garge N, Zhang X, Sun W, O’Connell TM, Bunger MK, Bultman SJ. 2011. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab 13:517–526. doi: 10.1016/j.cmet.2011.02.018. [DOI] [PMC free article] [PubMed] [Google Scholar]
6.De Vadder F, Kovatcheva-Datchary P, Goncalves D, Vinera J, Zitoun C, Duchampt A, Bäckhed F, Mithieux G. 2014. Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits. Cell 156:84–96. doi: 10.1016/j.cell.2013.12.016. [DOI] [PubMed] [Google Scholar]
7.Sahuri-Arisoylu M, Brody LP, Parkinson JR, Parkes H, Navaratnam N, Miller AD, Thomas EL, Frost G, Bell JD. 2016. Reprogramming of hepatic fat accumulation and ‘browning’ of adipose tissue by the short-chain fatty acid acetate. Int J Obes (Lond) 40:955–963. doi: 10.1038/ijo.2016.23. [DOI] [PubMed] [Google Scholar]
8.Morrison DJ, Preston T. 2016. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes 7:189–200. doi: 10.1080/19490976.2015.1134082. [DOI] [PMC free article] [PubMed] [Google Scholar]
9.Byndloss MX, Pernitzsch SR, Bäumler AJ. 2018. Healthy hosts rule within: ecological forces shaping the gut microbiota. Mucosal Immunol 11:1299–1305. doi: 10.1038/s41385-018-0010-y. [DOI] [PubMed] [Google Scholar]
10.Lloyd-Price J, Abu-Ali G, Huttenhower C. 2016. The healthy human microbiome. Genome Med 8:51. doi: 10.1186/s13073-016-0307-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
11.Ivanov II, Frutos R, Manel N, Yoshinaga K, Rifkin DB, Sartor RB, Finlay BB, Littman DR. 2008. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 4:337–349. doi: 10.1016/j.chom.2008.09.009. [DOI] [PMC free article] [PubMed] [Google Scholar]
12.Schachter J, Alvarinho de Oliveira D, da Silva CM, de Barros Alencar ACM, Duarte M, da Silva MMP, Ignácio A, Lopes-Torres EJ. 2020. Whipworm Infection promotes bacterial invasion, intestinal microbiota imbalance, and cellular immunomodulation. Infect Immun 88:e00642-19. doi: 10.1128/IAI.00642-19. [DOI] [PMC free article] [PubMed] [Google Scholar]
13.León ED, Francino MP. 2022. Roles of secretory immunoglobulin A in host-microbiota interactions in the gut ecosystem. Front Microbiol 13:880484. doi: 10.3389/fmicb.2022.880484. [DOI] [PMC free article] [PubMed] [Google Scholar]
14.Plata G, Baxter NT, Susanti D, Volland-Munson A, Gangaiah D, Nagireddy A, Mane SP, Balakuntla J, Hawkins TB, Kumar Mahajan A. 2022. Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome. Commun Biol 5:293. doi: 10.1038/s42003-022-03239-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
15.Hossain MD, Bulbul SM, Nishibori M, Islam MA. 2008. Effect of different growth promoters on growth and meat yield of broilers. J Poult Sci 45:287–291. doi: 10.2141/jpsa.45.287. [DOI] [Google Scholar]
16.Barros R, Vieira SL, Favero A, Taschetto D, Mascarello NC, Cemin H. 2012. Reassessing flavophospholipol effects on broiler performance. R Bras Zootec 41:2458–2462. doi: 10.1590/S1516-35982012001200011. [DOI] [Google Scholar]
17.Castanon JIR. 2007. History of the use of antibiotic as growth promoters in European poultry feeds. Poult Sci 86:2466–2471. doi: 10.3382/ps.2007-00249. [DOI] [PubMed] [Google Scholar]
18.Jha R, Mishra P. 2021. Dietary fiber in poultry nutrition and their effects on nutrient utilization, performance, gut health, and on the environment: a review. J Anim Sci Biotechnol 12:51. doi: 10.1186/s40104-021-00576-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
19.Hou L, Sun B, Yang Y. 2020. Effects of added dietary fiber and rearing system on the gut microbial diversity and gut health of chickens. Animals (Basel) 10:107. doi: 10.3390/ani10010107. [DOI] [PMC free article] [PubMed] [Google Scholar]
20.Cui Y, Diao ZP, Fan WT, Wei JL, Zhou JS, Zhu HY, Li DS, Guo LW, Tian YM, Song H, Su YH. 2022. Effects of dietary inclusion of alfalfa meal on laying performance, egg quality, intestinal morphology, caecal microbiota and metabolites in Zhuanghe Dagu chickens. Ital J Anim Sci 21:831–846. doi: 10.1080/1828051X.2022.2067009. [DOI] [Google Scholar]
21.Röhe I, Zentek J. 2021. Lignocellulose as an insoluble fiber source in poultry nutrition: a review. J Anim Sci Biotechnol 12:82. doi: 10.1186/s40104-021-00594-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
22.Hao Y, Wang X, Yuan S, Wang Y, Liao X, Zhong M, He Q, Shen H, Liao W, Shen J. 2021. Flammulina velutipes polysaccharide improves C57BL/6 mice gut health through regulation of intestine microbial metabolic activity. Int J Biol Macromol 167:1308–1318. doi: 10.1016/j.ijbiomac.2020.11.085. [DOI] [PubMed] [Google Scholar]
23.Zhang T, Ye J, Xue C, Wang Y, Liao W, Mao L, Yuan M, Lian S. 2018. Structural characteristics and bioactive properties of a novel polysaccharide from Flammulina velutipes. Carbohydr Polym 197:147–156. doi: 10.1016/j.carbpol.2018.05.069. [DOI] [PubMed] [Google Scholar]
24.Association CEF. 2019. Production data for Chinese Flammulina velutipes. http://bigdata.cefa.org.cn/.
25.Mahfuz S, Song H, Liu Z, Liu X, Diao Z, Ren G, Guo Z, Cui Y. 2018. Effect of golden needle mushroom (Flammulina velutipes) stem waste on laying performance, calcium utilization, immune response and serum immunity at early phase of production. Asian-Australas J Anim Sci 31:705–711. doi: 10.5713/ajas.17.0787. [DOI] [PMC free article] [PubMed] [Google Scholar]
26.Mahfuz SU, Chen M, Zhou JS, Wang S, Wei J, Liu Z, Song H. 2018. Evaluation of golden needle mushroom (Flammulina velutipes) stem waste on pullet performance and immune response. SA J an Sci 48:563–571. doi: 10.4314/sajas.v48i3.17. [DOI] [Google Scholar]
27.Mahfuz S, He T, Liu S, Wu D, Long S, Piao X. 2019. Dietary inclusion of mushroom (Flammulina velutipes) stem waste on growth performance, antibody response, immune status, and serum cholesterol in broiler chickens. Animals (Basel) 9:692. doi: 10.3390/ani9090692. [DOI] [PMC free article] [PubMed] [Google Scholar]
28.Chen M, Mahfuz S, Cui Y, Jia L, Liu Z, Song H. 2019. The antioxidant status of serum and egg yolk in layer fed with mushroom stembase (Flammulina velutipes). Pak J Zool 52:389–392. doi: 10.17582/journal.pjz/2020.52.1.sc6. [DOI] [Google Scholar]
29.Lu J, Idris U, Harmon B, Hofacre C, Maurer JJ, Lee MD. 2003. Diversity and succession of the intestinal bacterial community of the maturing broiler chicken. Appl Environ Microbiol 69:6816–6824. doi: 10.1128/AEM.69.11.6816-6824.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
30.Flint HJ, Duncan SH, Louis P. 2017. The impact of nutrition on intestinal bacterial communities. Curr Opin Microbiol 38:59–65. doi: 10.1016/j.mib.2017.04.005. [DOI] [PubMed] [Google Scholar]
31.Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y-Y, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. 2011. Linking long-term dietary patterns with gut microbial enterotypes. Science 334:105–108. doi: 10.1126/science.1208344. [DOI] [PMC free article] [PubMed] [Google Scholar]
32.Shang H, Zhao J, Dong X, Guo Y, Zhang H, Cheng J, Zhou H. 2020. Inulin improves the egg production performance and affects the cecum microbiota of laying hens. Int J Biol Macromol 155:1599–1609. doi: 10.1016/j.ijbiomac.2019.11.137. [DOI] [PubMed] [Google Scholar]
33.Chen X, Ma W, Hu N, Yan Y, Zhu Y, Wang Z, Jiao G, Chen X. 2021. Effects of alkaline protease on the production performance, egg quality, and cecal microbiota of hens during late laying period. Anim Sci J 92:e13658. doi: 10.1111/asj.13658. [DOI] [PubMed] [Google Scholar]
34.Zhang G, Wang H, Zhang J, Tang X, Raheem A, Wang M, Lin W, Liang L, Qi Y, Zhu Y, Jia Y, Cui S, Qin T. 2021. Modulatory effects of Bacillus subtilis on the performance, morphology, cecal microbiota and gut barrier function of laying hens. Animals (Basel) 11:1523. doi: 10.3390/ani11061523. [DOI] [PMC free article] [PubMed] [Google Scholar]
35.Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. 2016. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 165:1332–1345. doi: 10.1016/j.cell.2016.05.041. [DOI] [PubMed] [Google Scholar]
36.Kelly CJ, Zheng L, Campbell EL, Saeedi B, Scholz CC, Bayless AJ, Wilson KE, Glover LE, Kominsky DJ, Magnuson A, Weir TL, Ehrentraut SF, Pickel C, Kuhn KA, Lanis JM, Nguyen V, Taylor CT, Colgan SP. 2015. Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function. Cell Host Microbe 17:662–671. doi: 10.1016/j.chom.2015.03.005. [DOI] [PMC free article] [PubMed] [Google Scholar]
37.Mann EH, Gabryšová L, Pfeffer PE, O’Garra A, Hawrylowicz CM. 2019. High-dose IL-2 skews a glucocorticoid-driven IL-17 IL-10 memory CD4 T cell response towards a single IL-10-producing phenotype. J Immunol 202:684–693. doi: 10.4049/jimmunol.1800697. [DOI] [PMC free article] [PubMed] [Google Scholar]
38.Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, Scott K, Stanton C, Swanson KS, Cani PD, Verbeke K, Reid G. 2017. Expert consensus document: the International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol 14:491–502. doi: 10.1038/nrgastro.2017.75. [DOI] [PubMed] [Google Scholar]
39.Blakeley-Ruiz JA, Erickson AR, Cantarel BL, Xiong W, Adams R, Jansson JK, Fraser CM, Hettich RL. 2019. Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes. Microbiome 7:18. doi: 10.1186/s40168-019-0631-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
40.Tolnai E, Fauszt P, Fidler G, Pesti-Asboth G, Szilagyi E, Stagel A, Konya J, Szabo J, Stundl L, Babinszky L, Remenyik J, Biro S, Paholcsek M. 2021. Nutraceuticals induced changes in the broiler gastrointestinal tract microbiota. mSystems 6:e01124-20. doi: 10.1128/mSystems.01124-20. [DOI] [PMC free article] [PubMed] [Google Scholar]
41.Ngunjiri JM, Taylor KJM, Abundo MC, Jang H, Elaish M, Kc M, Ghorbani A, Wijeratne S, Weber BP, Johnson TJ, Lee C-W. 2019. Farm stage, bird age, and body site dominantly affect the quantity, taxonomic composition, and dynamics of respiratory and gut microbiota of commercial layer chickens. Appl Environ Microbiol 85:e03137-18. doi: 10.1128/AEM.03137-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
42.Sun B, Hou L, Yang Y. 2021. Effects of adding eubiotic lignocellulose on the growth performance, laying performance, gut microbiota, and short-chain fatty acids of two breeds of hens. Front Vet Sci 8:668003. doi: 10.3389/fvets.2021.668003. [DOI] [PMC free article] [PubMed] [Google Scholar]
43.Wanzenbock E, Zitz U, Steinbauer C, Kneifel W, Domig KJ, Schedle K. 2020. A diet containing native or fermented wheat bran does not interfere with natural microbiota of laying hens. Animal 14:1147–1155. doi: 10.1017/S1751731119003343. [DOI] [PubMed] [Google Scholar]
44.Wang J, Singh AK, Kong F, Kim WK. 2021. Effect of almond hulls as an alternative ingredient on broiler performance, nutrient digestibility, and cecal microbiota diversity. Poult Sci 100:100853. doi: 10.1016/j.psj.2020.11.030. [DOI] [PMC free article] [PubMed] [Google Scholar]
45.Dunkley KD, Dunkley CS, Njongmeta NL, Callaway TR, Hume ME, Kubena LF, Nisbet DJ, Ricke SC. 2007. Comparison of in vitro fermentation and molecular microbial profiles of high-fiber feed substrates incubated with chicken cecal inocula. Poult Sci 86:801–810. doi: 10.1093/ps/86.5.801. [DOI] [PubMed] [Google Scholar]
46.Mysara M, Berkell M, Xavier BB, De Backer S, Lammens C, Hautekiet V, Petkov S, Goossens H, Kumar-Singh S, Malhotra-Kumar S. 2021. Assessing the impact of flavophospholipol and virginiamycin supplementation on the broiler microbiota: a prospective controlled intervention study. mSystems 6:e00381-21. doi: 10.1128/mSystems.00381-21. [DOI] [PMC free article] [PubMed] [Google Scholar]
47.Neijat M, Habtewold J, Shirley RB, Welsher A, Barton J, Thiery P, Kiarie E. 2019. Strain DSM 29784 modulates the cecal microbiome, concentration of short-chain fatty acids, and apparent retention of dietary components in shaver white chickens during grower, developer, and laying phases. Appl Environ Microbiol 85:e00402-19. doi: 10.1128/AEM.00402-19. [DOI] [PMC free article] [PubMed] [Google Scholar]
48.Jurburg SD, Brouwer MSM, Ceccarelli D, van der Goot J, Jansman AJM, Bossers A. 2019. Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession. Microbiologyopen 8:e00821. doi: 10.1002/mbo3.821. [DOI] [PMC free article] [PubMed] [Google Scholar]
49.Oh BS, Kim J-S, Yu Sy Ryu SW, Park S-H, Kang SW, Park J-E, Choi S-H, Han K-I, Lee KC, Eom MK, Suh MK, Kim HS, Lee DH, Yoon H, Kim B-Y, Lee JH, Lee J-S, Lee JH. 2020. Sutterella faecalis sp. nov., isolated from human faeces. J Microbiol 58:99–104. doi: 10.1007/s12275-020-9396-9. [DOI] [PubMed] [Google Scholar]
50.Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C. 2015. Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biol 16:67. doi: 10.1186/s13059-015-0637-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
51.Butera A, Di Paola M, Vitali F, De Nitto D, Covotta F, Borrini F, Pica R, De Filippo C, Cavalieri D, Giuliani A, Pronio A, Boirivant M. 2020. IL-13 mRNA tissue content identifies two subsets of adult ulcerative colitis patients with different clinical and mucosa-associated microbiota profiles. J Crohns Colitis 14:369–380. doi: 10.1093/ecco-jcc/jjz154. [DOI] [PubMed] [Google Scholar]
52.Cui Z, Wu S, Li J, Yang Q-E, Chai S, Wang L, Wang X, Zhang X, Liu S, Yao J. 2020. Effect of alfalfa hay and starter feeding intervention on gastrointestinal microbial community, growth and immune performance of yak calves. Front Microbiol 11:994. doi: 10.3389/fmicb.2020.00994. [DOI] [PMC free article] [PubMed] [Google Scholar]
53.Yi Y, Shen L, Shi W, Xia F, Zhang H, Wang Y, Zhang J, Wang Y, Sun X, Zhang Z, Zou W, Yang W, Zhang L, Zhu J, Goel A, Ma Y, Zhang Z. 2021. Gut microbiome components predict response to neoadjuvant chemoradiotherapy in patients with locally advanced rectal cancer: a prospective, longitudinal study. Clin Cancer Res 27:1329–1340. doi: 10.1158/1078-0432.CCR-20-3445. [DOI] [PubMed] [Google Scholar]
54.Lee J-Y, Kang W, Shin N-R, Hyun D-W, Kim PS, Kim HS, Lee J-Y, Tak EJ, Sung H, Bae J-W. 2021. Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria [sic] isolated from faeces of a patient with Crohn’s disease. Int J Syst Evol Microbiol 71. doi: 10.1099/ijsem.0.005129. [DOI] [PubMed] [Google Scholar]
55.Vandeputte D, Falony G, Vieira-Silva S, Wang J, Sailer M, Theis S, Verbeke K, Raes J. 2017. Prebiotic inulin-type fructans induce specific changes in the human gut microbiota. Gut 66:1968–1974. doi: 10.1136/gutjnl-2016-313271. [DOI] [PMC free article] [PubMed] [Google Scholar]
56.Shetty SA, Boeren S, Bui TPN, Smidt H, de Vos WM. 2020. Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics. Environ Microbiol 22:4863–4875. doi: 10.1111/1462-2920.15269. [DOI] [PMC free article] [PubMed] [Google Scholar]
57.Kampik C, Liu N, Mroueh M, Franche N, Borne R, Denis Y, Gagnot S, Tardif C, Pagès S, Perret S, Vita N, de Philip P, Fierobe H-P. 2021. Handling several sugars at a time: a case study of xyloglucan utilization by Ruminiclostridium cellulolyticum. mBio 12:e02206-21. doi: 10.1128/mBio.02206-21. [DOI] [PMC free article] [PubMed] [Google Scholar]
58.Ren Z, You W, Wu S, Poetsch A, Xu C. 2019. Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation. Biotechnol Biofuels 12:183. doi: 10.1186/s13068-019-1522-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
59.Wang L, Liao Y, Yang R, Zhu Z, Zhang L, Wu Z, Sun X. 2021. An engineered probiotic secreting Sj16 ameliorates colitis via Ruminococcaceae/butyrate/retinoic acid axis. Bioeng Transl Med 6:e10219. doi: 10.1002/btm2.10219. [DOI] [PMC free article] [PubMed] [Google Scholar]
60.Morais-Silva FO, Rezende AM, Pimentel C, Santos CI, Clemente C, Varela-Raposo A, Resende DM, da Silva SM, de Oliveira LM, Matos M, Costa DA, Flores O, Ruiz JC, Rodrigues-Pousada C. 2014. Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus. Microbiologyopen 3:513–530. doi: 10.1002/mbo3.184. [DOI] [PMC free article] [PubMed] [Google Scholar]
61.Zhang WW, Gritsenko MA, Moore RJ, Culley DE, Nie L, Petritis K, Strittmatter EF, Camp DG, Smith RD, Brockman FJ. 2006. A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry. Proteomics 6:4286–4299. doi: 10.1002/pmic.200500930. [DOI] [PubMed] [Google Scholar]
62.Pereira PM, He Q, Valente FMA, Xavier AV, Zhou JZ, Pereira IAC, Louro RO. 2008. Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis. Antonie Van Leeuwenhoek 93:347–362. doi: 10.1007/s10482-007-9212-0. [DOI] [PubMed] [Google Scholar]
63.Coutinho CMLM, Coutinho-Silva R, Zinkevich V, Pearce CB, Ojcius DM, Beech I. 2017. Sulphate-reducing bacteria from ulcerative colitis patients induce apoptosis of gastrointestinal epithelial cells. Microb Pathog 112:126–134. doi: 10.1016/j.micpath.2017.09.054. [DOI] [PubMed] [Google Scholar]
64.Rowan F, Docherty NG, Murphy M, Murphy B, Calvin Coffey J, O’Connell PR. 2010. Desulfovibrio bacterial species are increased in ulcerative colitis. Dis Colon Rectum 53:1530–1536. doi: 10.1007/DCR.0b013e3181f1e620. [DOI] [PubMed] [Google Scholar]
65.Loubinoux J, Bronowicki J-P, Pereira IAC, Mougenel J-L, Faou AE. 2002. Sulfate-reducing bacteria in human feces and their association with inflammatory bowel diseases. FEMS Microbiol Ecol 40:107–112. doi: 10.1111/j.1574-6941.2002.tb00942.x. [DOI] [PubMed] [Google Scholar]
66.Oh JK, Chae JP, Pajarillo EAB, Kim SH, Kwak M-J, Eun J-S, Chee SW, Whang K-Y, Kim S-H, Kang D-K. 2020. Association between the body weight of growing pigs and the functional capacity of their gut microbiota. Anim Sci J 91:e13418. doi: 10.1111/asj.13418. [DOI] [PubMed] [Google Scholar]
67.Huang J, Huang J, Li Y, Wang Y, Wang F, Qiu X, Liu X, Li H. 2021. Sodium alginate modulates immunity, intestinal mucosal barrier function, and gut microbiota in cyclophosphamide-induced immunosuppressed BALB/c mice. J Agric Food Chem 69:7064–7073. doi: 10.1021/acs.jafc.1c02294. [DOI] [PubMed] [Google Scholar]
68.Wu S, Zuo J, Cheng Y, Zhang Y, Zhang Z, Wu M, Yang Y, Tong H. 2021. Ethanol extract of Sargarsum fusiforme alleviates HFD/STZ-induced hyperglycemia in association with modulation of gut microbiota and intestinal metabolites in type 2 diabetic mice. Food Res Int 147:110550. doi: 10.1016/j.foodres.2021.110550. [DOI] [PubMed] [Google Scholar]
69.Pontifex MG, Mushtaq A, Le Gall G, Rodriguez-Ramiro I, Blokker BA, Hoogteijling MEM, Ricci M, Pellizzon M, Vauzour D, Müller M. 2021. Differential influence of soluble dietary fibres on intestinal and hepatic carbohydrate response. Nutrients 13:4278. doi: 10.3390/nu13124278. [DOI] [PMC free article] [PubMed] [Google Scholar]
70.Xing Z, Li H, Li M, Gao R, Guo C, Mi S. 2021. Disequilibrium in chicken gut microflora with avian colibacillosis is related to microenvironment damaged by antibiotics. Sci Total Environ 762:143058. doi: 10.1016/j.scitotenv.2020.143058. [DOI] [PubMed] [Google Scholar]
71.Forbes JD, Chen C-Y, Knox NC, Marrie R-A, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN, Van Domselaar G. 2018. A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist? Microbiome 6:221. doi: 10.1186/s40168-018-0603-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
72.Leung H, Arrazola A, Torrey S, Kiarie E. 2018. Utilization of soy hulls, oat hulls, and flax meal fiber in adult broiler breeder hens. Poult Sci 97:1368–1372. doi: 10.3382/ps/pex434. [DOI] [PubMed] [Google Scholar]
73.Kheravii SK, Swick RA, Choct M, Wu S-B. 2018. Effect of oat hulls as a free choice feeding on broiler performance, short chain fatty acids and microflora under a mild necrotic enteritis challenge. Anim Nutr 4:65–72. doi: 10.1016/j.aninu.2017.11.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
74.Chuang WY, Lin LJ, Shih HD, Shy YM, Chang SC, Lee TT. 2021. Intestinal microbiota, anti-inflammatory, and anti-oxidative status of broiler chickens fed diets containing mushroom waste compost by-products. Animals (Basel) 11:2550. doi: 10.3390/ani11092550. [DOI] [PMC free article] [PubMed] [Google Scholar]
75.Wen C, Yan W, Mai C, Duan Z, Zheng J, Sun C, Yang N. 2021. Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens. Microbiome 9:126. doi: 10.1186/s40168-021-01040-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
76.Wen C, Yan W, Sun C, Ji C, Zhou Q, Zhang D, Zheng J, Yang N. 2019. The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens. ISME J 13:1422–1436. doi: 10.1038/s41396-019-0367-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
77.Aragón-Vela J, Solis-Urra P, Ruiz-Ojeda FJ, Álvarez-Mercado AI, Olivares-Arancibia J, Plaza-Diaz J. 2021. Impact of exercise on gut microbiota in obesity. Nutrients 13:3999. doi: 10.3390/nu13113999. [DOI] [PMC free article] [PubMed] [Google Scholar]
78.Terrapon N, Henrissat B. 2014. How do gut microbes break down dietary fiber? Trends Biochem Sci 39:156–158. doi: 10.1016/j.tibs.2014.02.005. [DOI] [PubMed] [Google Scholar]
79.Coyte KZ, Schluter J, Foster KR. 2015. The ecology of the microbiome: networks, competition, and stability. Science 350:663–666. doi: 10.1126/science.aad2602. [DOI] [PubMed] [Google Scholar]
80.Walugembe M, Hsieh JCF, Koszewski NJ, Lamont SJ, Persia ME, Rothschild MF. 2015. Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of broiler and laying-hen chicks. Poult Sci 94:2351–2359. doi: 10.3382/ps/pev242. [DOI] [PubMed] [Google Scholar]
81.Cui X, Gou Z, Jiang Z, Li L, Lin X, Fan Q, Wang Y, Jiang S. 2022. Dietary fiber modulates abdominal fat deposition associated with cecal microbiota and metabolites in yellow chickens. Poult Sci 101:101721. doi: 10.1016/j.psj.2022.101721. [DOI] [PMC free article] [PubMed] [Google Scholar]
82.Sivaprakasam S, Prasad PD, Singh N. 2016. Benefits of short-chain fatty acids and their receptors in inflammation and carcinogenesis. Pharmacol Ther 164:144–151. doi: 10.1016/j.pharmthera.2016.04.007. [DOI] [PMC free article] [PubMed] [Google Scholar]
83.Röhe I, Vahjen W, Metzger F, Zentek J. 2020. Effect of a “diluted” diet containing 10% lignocellulose on the gastrointestinal tract, intestinal microbiota, and excreta characteristics of dual purpose laying hens. Poult Sci 99:310–319. doi: 10.3382/ps/pez492. [DOI] [PMC free article] [PubMed] [Google Scholar]
84.Tomova A, Bukovsky I, Rembert E, Yonas W, Alwarith J, Barnard ND, Kahleova H. 2019. The effects of vegetarian and vegan diets on gut microbiota. Front Nutr 6:47. doi: 10.3389/fnut.2019.00047. [DOI] [PMC free article] [PubMed] [Google Scholar]
85.Wu W, Sun M, Chen F, Cao AT, Liu H, Zhao Y, Huang X, Xiao Y, Yao S, Zhao Q, Liu Z, Cong Y. 2017. Microbiota metabolite short-chain fatty acid acetate promotes intestinal IgA response to microbiota which is mediated by GPR43. Mucosal Immunol 10:946–956. doi: 10.1038/mi.2016.114. [DOI] [PMC free article] [PubMed] [Google Scholar]
86.Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, Marsland BJ. 2014. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 20:159–166. doi: 10.1038/nm.3444. [DOI] [PubMed] [Google Scholar]
87.Haghikia A, Jörg S, Duscha A, Berg J, Manzel A, Waschbisch A, Hammer A, Lee D-H, May C, Wilck N, Balogh A, Ostermann AI, Schebb NH, Akkad DA, Grohme DA, Kleinewietfeld M, Kempa S, Thöne J, Demir S, Müller DN, Gold R, Linker RA. 2016. Dietary fatty acids directly impact central nervous system autoimmunity via the small intestine. Immunity 44:951–953. doi: 10.1016/j.immuni.2016.04.006. [DOI] [PubMed] [Google Scholar]
88.James KR, Gomes T, Elmentaite R, Kumar N, Gulliver EL, King HW, Stares MD, Bareham BR, Ferdinand JR, Petrova VN, Polański K, Forster SC, Jarvis LB, Suchanek O, Howlett S, James LK, Jones JL, Meyer KB, Clatworthy MR, Saeb-Parsy K, Lawley TD, Teichmann SA. 2020. Distinct microbial and immune niches of the human colon. Nat Immunol 21:343–353. doi: 10.1038/s41590-020-0602-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
89.Lin WC, Lee TT. 2020. Laetiporus sulphureus-fermented wheat bran enhanced the broiler growth performance by improving the intestinal microflora and inflammation status. Poult Sci 99:3606–3616. doi: 10.1016/j.psj.2020.04.011. [DOI] [PMC free article] [PubMed] [Google Scholar]
90.Yang Y, Palm NW. 2020. Immunoglobulin A and the microbiome. Curr Opin Microbiol 56:89–96. doi: 10.1016/j.mib.2020.08.003. [DOI] [PubMed] [Google Scholar]
91.Min YN, Yang HL, Xu YX, Gao YP. 2016. Effects of dietary supplementation of synbiotics on growth performance, intestinal morphology, sIgA content and antioxidant capacities of broilers. J Anim Physiol Anim Nutr (Berl) 100:1073–1080. doi: 10.1111/jpn.12479. [DOI] [PubMed] [Google Scholar]
92.Shang Q, Liu H, Wu D, Mahfuz S, Piao X. 2021. Source of fiber influences growth, immune responses, gut barrier function and microbiota in weaned piglets fed antibiotic-free diets. Anim Nutr 7:315–325. doi: 10.1016/j.aninu.2020.12.008. [DOI] [PMC free article] [PubMed] [Google Scholar]
93.Ding XM, Li DD, Bai SP, Wang JP, Zeng QF, Su ZW, Xuan Y, Zhang KY. 2018. Effect of dietary xylooligosaccharides on intestinal characteristics, gut microbiota, cecal short-chain fatty acids, and plasma immune parameters of laying hens. Poult Sci 97:874–881. doi: 10.3382/ps/pex372. [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

FIG S1

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

FIG S2

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

FIG S3

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

TABLE S1

Nutrients of Flammulina velutipes stipe waste (air-dried basis, percent). Download Table S1, DOCX file, 0.02 MB^{(19.8KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

TABLE S2

Starter phase (0 to 28 days) composition and nutrient levels of diets (air-dried basis, percent). Download Table S2, DOCX file, 0.02 MB^{(21.3KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

TABLE S3

Grower phase (29 to 70 days) composition and nutrient levels of diets (air-dried basis, percent). Download Table S3, DOCX file, 0.02 MB^{(21.3KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

TABLE S4

Developer phase (71 to 112 days) composition and nutrient levels of diets (air-dried basis, percent). Download Table S4, DOCX file, 0.02 MB^{(21.2KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

TABLE S5

Finisher phase (113 to 490 days) composition and nutrient levels of diets (air-dried basis, percent). Download Table S5, DOCX file, 0.02 MB^{(21.3KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

Reviewer comments

reviewer-comments.pdf^{(557.2KB, pdf)}

Data Availability Statement

Sequence data generated in this study have been made available at the Sequence Read Archive (SRA) on NCBI under project number PRJNA628749.

TABLE S3

Grower phase (29 to 70 days) composition and nutrient levels of diets (air-dried basis, percent). Download Table S3, DOCX file, 0.02 MB^{(21.3KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

TABLE S4

Developer phase (71 to 112 days) composition and nutrient levels of diets (air-dried basis, percent). Download Table S4, DOCX file, 0.02 MB^{(21.2KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

TABLE S5

Finisher phase (113 to 490 days) composition and nutrient levels of diets (air-dried basis, percent). Download Table S5, DOCX file, 0.02 MB^{(21.3KB, docx)}.

This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

[B1] 1.Sommer F, Bäckhed F. 2013. The gut microbiota—masters of host development and physiology. Nat Rev Microbiol 11:227–238. doi: 10.1038/nrmicro2974. [DOI] [PubMed] [Google Scholar]

[B2] 2.van der Hee B, Wells JM. 2021. Microbial regulation of host physiology by short-chain fatty acids. Trends Microbiol 29:700–712. doi: 10.1016/j.tim.2021.02.001. [DOI] [PubMed] [Google Scholar]

[B3] 3.Cani PD, Van Hul M, Lefort C, Depommier C, Rastelli M, Everard A. 2019. Microbial regulation of organismal energy homeostasis. Nat Metab 1:34–46. doi: 10.1038/s42255-018-0017-4. [DOI] [PubMed] [Google Scholar]

[B4] 4.Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. 2014. The Carbohydrate-Active Enzymes database (CAZy) in 2013. Nucleic Acids Res 42:D490–D495. doi: 10.1093/nar/gkt1178. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B5] 5.Donohoe DR, Garge N, Zhang X, Sun W, O’Connell TM, Bunger MK, Bultman SJ. 2011. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab 13:517–526. doi: 10.1016/j.cmet.2011.02.018. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B6] 6.De Vadder F, Kovatcheva-Datchary P, Goncalves D, Vinera J, Zitoun C, Duchampt A, Bäckhed F, Mithieux G. 2014. Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits. Cell 156:84–96. doi: 10.1016/j.cell.2013.12.016. [DOI] [PubMed] [Google Scholar]

[B7] 7.Sahuri-Arisoylu M, Brody LP, Parkinson JR, Parkes H, Navaratnam N, Miller AD, Thomas EL, Frost G, Bell JD. 2016. Reprogramming of hepatic fat accumulation and ‘browning’ of adipose tissue by the short-chain fatty acid acetate. Int J Obes (Lond) 40:955–963. doi: 10.1038/ijo.2016.23. [DOI] [PubMed] [Google Scholar]

[B8] 8.Morrison DJ, Preston T. 2016. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes 7:189–200. doi: 10.1080/19490976.2015.1134082. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B9] 9.Byndloss MX, Pernitzsch SR, Bäumler AJ. 2018. Healthy hosts rule within: ecological forces shaping the gut microbiota. Mucosal Immunol 11:1299–1305. doi: 10.1038/s41385-018-0010-y. [DOI] [PubMed] [Google Scholar]

[B10] 10.Lloyd-Price J, Abu-Ali G, Huttenhower C. 2016. The healthy human microbiome. Genome Med 8:51. doi: 10.1186/s13073-016-0307-y. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B11] 11.Ivanov II, Frutos R, Manel N, Yoshinaga K, Rifkin DB, Sartor RB, Finlay BB, Littman DR. 2008. Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 4:337–349. doi: 10.1016/j.chom.2008.09.009. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B12] 12.Schachter J, Alvarinho de Oliveira D, da Silva CM, de Barros Alencar ACM, Duarte M, da Silva MMP, Ignácio A, Lopes-Torres EJ. 2020. Whipworm Infection promotes bacterial invasion, intestinal microbiota imbalance, and cellular immunomodulation. Infect Immun 88:e00642-19. doi: 10.1128/IAI.00642-19. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B13] 13.León ED, Francino MP. 2022. Roles of secretory immunoglobulin A in host-microbiota interactions in the gut ecosystem. Front Microbiol 13:880484. doi: 10.3389/fmicb.2022.880484. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B14] 14.Plata G, Baxter NT, Susanti D, Volland-Munson A, Gangaiah D, Nagireddy A, Mane SP, Balakuntla J, Hawkins TB, Kumar Mahajan A. 2022. Growth promotion and antibiotic induced metabolic shifts in the chicken gut microbiome. Commun Biol 5:293. doi: 10.1038/s42003-022-03239-6. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B15] 15.Hossain MD, Bulbul SM, Nishibori M, Islam MA. 2008. Effect of different growth promoters on growth and meat yield of broilers. J Poult Sci 45:287–291. doi: 10.2141/jpsa.45.287. [DOI] [Google Scholar]

[B16] 16.Barros R, Vieira SL, Favero A, Taschetto D, Mascarello NC, Cemin H. 2012. Reassessing flavophospholipol effects on broiler performance. R Bras Zootec 41:2458–2462. doi: 10.1590/S1516-35982012001200011. [DOI] [Google Scholar]

[B17] 17.Castanon JIR. 2007. History of the use of antibiotic as growth promoters in European poultry feeds. Poult Sci 86:2466–2471. doi: 10.3382/ps.2007-00249. [DOI] [PubMed] [Google Scholar]

[B18] 18.Jha R, Mishra P. 2021. Dietary fiber in poultry nutrition and their effects on nutrient utilization, performance, gut health, and on the environment: a review. J Anim Sci Biotechnol 12:51. doi: 10.1186/s40104-021-00576-0. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B19] 19.Hou L, Sun B, Yang Y. 2020. Effects of added dietary fiber and rearing system on the gut microbial diversity and gut health of chickens. Animals (Basel) 10:107. doi: 10.3390/ani10010107. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B20] 20.Cui Y, Diao ZP, Fan WT, Wei JL, Zhou JS, Zhu HY, Li DS, Guo LW, Tian YM, Song H, Su YH. 2022. Effects of dietary inclusion of alfalfa meal on laying performance, egg quality, intestinal morphology, caecal microbiota and metabolites in Zhuanghe Dagu chickens. Ital J Anim Sci 21:831–846. doi: 10.1080/1828051X.2022.2067009. [DOI] [Google Scholar]

[B21] 21.Röhe I, Zentek J. 2021. Lignocellulose as an insoluble fiber source in poultry nutrition: a review. J Anim Sci Biotechnol 12:82. doi: 10.1186/s40104-021-00594-y. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B22] 22.Hao Y, Wang X, Yuan S, Wang Y, Liao X, Zhong M, He Q, Shen H, Liao W, Shen J. 2021. Flammulina velutipes polysaccharide improves C57BL/6 mice gut health through regulation of intestine microbial metabolic activity. Int J Biol Macromol 167:1308–1318. doi: 10.1016/j.ijbiomac.2020.11.085. [DOI] [PubMed] [Google Scholar]

[B23] 23.Zhang T, Ye J, Xue C, Wang Y, Liao W, Mao L, Yuan M, Lian S. 2018. Structural characteristics and bioactive properties of a novel polysaccharide from Flammulina velutipes. Carbohydr Polym 197:147–156. doi: 10.1016/j.carbpol.2018.05.069. [DOI] [PubMed] [Google Scholar]

[B24] 24.Association CEF. 2019. Production data for Chinese Flammulina velutipes. http://bigdata.cefa.org.cn/.

[B25] 25.Mahfuz S, Song H, Liu Z, Liu X, Diao Z, Ren G, Guo Z, Cui Y. 2018. Effect of golden needle mushroom (Flammulina velutipes) stem waste on laying performance, calcium utilization, immune response and serum immunity at early phase of production. Asian-Australas J Anim Sci 31:705–711. doi: 10.5713/ajas.17.0787. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B26] 26.Mahfuz SU, Chen M, Zhou JS, Wang S, Wei J, Liu Z, Song H. 2018. Evaluation of golden needle mushroom (Flammulina velutipes) stem waste on pullet performance and immune response. SA J an Sci 48:563–571. doi: 10.4314/sajas.v48i3.17. [DOI] [Google Scholar]

[B27] 27.Mahfuz S, He T, Liu S, Wu D, Long S, Piao X. 2019. Dietary inclusion of mushroom (Flammulina velutipes) stem waste on growth performance, antibody response, immune status, and serum cholesterol in broiler chickens. Animals (Basel) 9:692. doi: 10.3390/ani9090692. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B28] 28.Chen M, Mahfuz S, Cui Y, Jia L, Liu Z, Song H. 2019. The antioxidant status of serum and egg yolk in layer fed with mushroom stembase (Flammulina velutipes). Pak J Zool 52:389–392. doi: 10.17582/journal.pjz/2020.52.1.sc6. [DOI] [Google Scholar]

[B29] 29.Lu J, Idris U, Harmon B, Hofacre C, Maurer JJ, Lee MD. 2003. Diversity and succession of the intestinal bacterial community of the maturing broiler chicken. Appl Environ Microbiol 69:6816–6824. doi: 10.1128/AEM.69.11.6816-6824.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B30] 30.Flint HJ, Duncan SH, Louis P. 2017. The impact of nutrition on intestinal bacterial communities. Curr Opin Microbiol 38:59–65. doi: 10.1016/j.mib.2017.04.005. [DOI] [PubMed] [Google Scholar]

[B31] 31.Wu GD, Chen J, Hoffmann C, Bittinger K, Chen Y-Y, Keilbaugh SA, Bewtra M, Knights D, Walters WA, Knight R, Sinha R, Gilroy E, Gupta K, Baldassano R, Nessel L, Li H, Bushman FD, Lewis JD. 2011. Linking long-term dietary patterns with gut microbial enterotypes. Science 334:105–108. doi: 10.1126/science.1208344. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B32] 32.Shang H, Zhao J, Dong X, Guo Y, Zhang H, Cheng J, Zhou H. 2020. Inulin improves the egg production performance and affects the cecum microbiota of laying hens. Int J Biol Macromol 155:1599–1609. doi: 10.1016/j.ijbiomac.2019.11.137. [DOI] [PubMed] [Google Scholar]

[B33] 33.Chen X, Ma W, Hu N, Yan Y, Zhu Y, Wang Z, Jiao G, Chen X. 2021. Effects of alkaline protease on the production performance, egg quality, and cecal microbiota of hens during late laying period. Anim Sci J 92:e13658. doi: 10.1111/asj.13658. [DOI] [PubMed] [Google Scholar]

[B34] 34.Zhang G, Wang H, Zhang J, Tang X, Raheem A, Wang M, Lin W, Liang L, Qi Y, Zhu Y, Jia Y, Cui S, Qin T. 2021. Modulatory effects of Bacillus subtilis on the performance, morphology, cecal microbiota and gut barrier function of laying hens. Animals (Basel) 11:1523. doi: 10.3390/ani11061523. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B35] 35.Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. 2016. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 165:1332–1345. doi: 10.1016/j.cell.2016.05.041. [DOI] [PubMed] [Google Scholar]

[B36] 36.Kelly CJ, Zheng L, Campbell EL, Saeedi B, Scholz CC, Bayless AJ, Wilson KE, Glover LE, Kominsky DJ, Magnuson A, Weir TL, Ehrentraut SF, Pickel C, Kuhn KA, Lanis JM, Nguyen V, Taylor CT, Colgan SP. 2015. Crosstalk between microbiota-derived short-chain fatty acids and intestinal epithelial HIF augments tissue barrier function. Cell Host Microbe 17:662–671. doi: 10.1016/j.chom.2015.03.005. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B37] 37.Mann EH, Gabryšová L, Pfeffer PE, O’Garra A, Hawrylowicz CM. 2019. High-dose IL-2 skews a glucocorticoid-driven IL-17 IL-10 memory CD4 T cell response towards a single IL-10-producing phenotype. J Immunol 202:684–693. doi: 10.4049/jimmunol.1800697. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B38] 38.Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, Scott K, Stanton C, Swanson KS, Cani PD, Verbeke K, Reid G. 2017. Expert consensus document: the International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol 14:491–502. doi: 10.1038/nrgastro.2017.75. [DOI] [PubMed] [Google Scholar]

[B39] 39.Blakeley-Ruiz JA, Erickson AR, Cantarel BL, Xiong W, Adams R, Jansson JK, Fraser CM, Hettich RL. 2019. Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn’s remission patients despite temporal variations in microbial taxa, genomes, and proteomes. Microbiome 7:18. doi: 10.1186/s40168-019-0631-8. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B40] 40.Tolnai E, Fauszt P, Fidler G, Pesti-Asboth G, Szilagyi E, Stagel A, Konya J, Szabo J, Stundl L, Babinszky L, Remenyik J, Biro S, Paholcsek M. 2021. Nutraceuticals induced changes in the broiler gastrointestinal tract microbiota. mSystems 6:e01124-20. doi: 10.1128/mSystems.01124-20. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B41] 41.Ngunjiri JM, Taylor KJM, Abundo MC, Jang H, Elaish M, Kc M, Ghorbani A, Wijeratne S, Weber BP, Johnson TJ, Lee C-W. 2019. Farm stage, bird age, and body site dominantly affect the quantity, taxonomic composition, and dynamics of respiratory and gut microbiota of commercial layer chickens. Appl Environ Microbiol 85:e03137-18. doi: 10.1128/AEM.03137-18. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B42] 42.Sun B, Hou L, Yang Y. 2021. Effects of adding eubiotic lignocellulose on the growth performance, laying performance, gut microbiota, and short-chain fatty acids of two breeds of hens. Front Vet Sci 8:668003. doi: 10.3389/fvets.2021.668003. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B43] 43.Wanzenbock E, Zitz U, Steinbauer C, Kneifel W, Domig KJ, Schedle K. 2020. A diet containing native or fermented wheat bran does not interfere with natural microbiota of laying hens. Animal 14:1147–1155. doi: 10.1017/S1751731119003343. [DOI] [PubMed] [Google Scholar]

[B44] 44.Wang J, Singh AK, Kong F, Kim WK. 2021. Effect of almond hulls as an alternative ingredient on broiler performance, nutrient digestibility, and cecal microbiota diversity. Poult Sci 100:100853. doi: 10.1016/j.psj.2020.11.030. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B45] 45.Dunkley KD, Dunkley CS, Njongmeta NL, Callaway TR, Hume ME, Kubena LF, Nisbet DJ, Ricke SC. 2007. Comparison of in vitro fermentation and molecular microbial profiles of high-fiber feed substrates incubated with chicken cecal inocula. Poult Sci 86:801–810. doi: 10.1093/ps/86.5.801. [DOI] [PubMed] [Google Scholar]

[B46] 46.Mysara M, Berkell M, Xavier BB, De Backer S, Lammens C, Hautekiet V, Petkov S, Goossens H, Kumar-Singh S, Malhotra-Kumar S. 2021. Assessing the impact of flavophospholipol and virginiamycin supplementation on the broiler microbiota: a prospective controlled intervention study. mSystems 6:e00381-21. doi: 10.1128/mSystems.00381-21. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B47] 47.Neijat M, Habtewold J, Shirley RB, Welsher A, Barton J, Thiery P, Kiarie E. 2019. Strain DSM 29784 modulates the cecal microbiome, concentration of short-chain fatty acids, and apparent retention of dietary components in shaver white chickens during grower, developer, and laying phases. Appl Environ Microbiol 85:e00402-19. doi: 10.1128/AEM.00402-19. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B48] 48.Jurburg SD, Brouwer MSM, Ceccarelli D, van der Goot J, Jansman AJM, Bossers A. 2019. Patterns of community assembly in the developing chicken microbiome reveal rapid primary succession. Microbiologyopen 8:e00821. doi: 10.1002/mbo3.821. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B49] 49.Oh BS, Kim J-S, Yu Sy Ryu SW, Park S-H, Kang SW, Park J-E, Choi S-H, Han K-I, Lee KC, Eom MK, Suh MK, Kim HS, Lee DH, Yoon H, Kim B-Y, Lee JH, Lee J-S, Lee JH. 2020. Sutterella faecalis sp. nov., isolated from human faeces. J Microbiol 58:99–104. doi: 10.1007/s12275-020-9396-9. [DOI] [PubMed] [Google Scholar]

[B50] 50.Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C. 2015. Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biol 16:67. doi: 10.1186/s13059-015-0637-x. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B51] 51.Butera A, Di Paola M, Vitali F, De Nitto D, Covotta F, Borrini F, Pica R, De Filippo C, Cavalieri D, Giuliani A, Pronio A, Boirivant M. 2020. IL-13 mRNA tissue content identifies two subsets of adult ulcerative colitis patients with different clinical and mucosa-associated microbiota profiles. J Crohns Colitis 14:369–380. doi: 10.1093/ecco-jcc/jjz154. [DOI] [PubMed] [Google Scholar]

[B52] 52.Cui Z, Wu S, Li J, Yang Q-E, Chai S, Wang L, Wang X, Zhang X, Liu S, Yao J. 2020. Effect of alfalfa hay and starter feeding intervention on gastrointestinal microbial community, growth and immune performance of yak calves. Front Microbiol 11:994. doi: 10.3389/fmicb.2020.00994. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B53] 53.Yi Y, Shen L, Shi W, Xia F, Zhang H, Wang Y, Zhang J, Wang Y, Sun X, Zhang Z, Zou W, Yang W, Zhang L, Zhu J, Goel A, Ma Y, Zhang Z. 2021. Gut microbiome components predict response to neoadjuvant chemoradiotherapy in patients with locally advanced rectal cancer: a prospective, longitudinal study. Clin Cancer Res 27:1329–1340. doi: 10.1158/1078-0432.CCR-20-3445. [DOI] [PubMed] [Google Scholar]

[B54] 54.Lee J-Y, Kang W, Shin N-R, Hyun D-W, Kim PS, Kim HS, Lee J-Y, Tak EJ, Sung H, Bae J-W. 2021. Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria [sic] isolated from faeces of a patient with Crohn’s disease. Int J Syst Evol Microbiol 71. doi: 10.1099/ijsem.0.005129. [DOI] [PubMed] [Google Scholar]

[B55] 55.Vandeputte D, Falony G, Vieira-Silva S, Wang J, Sailer M, Theis S, Verbeke K, Raes J. 2017. Prebiotic inulin-type fructans induce specific changes in the human gut microbiota. Gut 66:1968–1974. doi: 10.1136/gutjnl-2016-313271. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B56] 56.Shetty SA, Boeren S, Bui TPN, Smidt H, de Vos WM. 2020. Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics. Environ Microbiol 22:4863–4875. doi: 10.1111/1462-2920.15269. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B57] 57.Kampik C, Liu N, Mroueh M, Franche N, Borne R, Denis Y, Gagnot S, Tardif C, Pagès S, Perret S, Vita N, de Philip P, Fierobe H-P. 2021. Handling several sugars at a time: a case study of xyloglucan utilization by Ruminiclostridium cellulolyticum. mBio 12:e02206-21. doi: 10.1128/mBio.02206-21. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B58] 58.Ren Z, You W, Wu S, Poetsch A, Xu C. 2019. Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation. Biotechnol Biofuels 12:183. doi: 10.1186/s13068-019-1522-8. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B59] 59.Wang L, Liao Y, Yang R, Zhu Z, Zhang L, Wu Z, Sun X. 2021. An engineered probiotic secreting Sj16 ameliorates colitis via Ruminococcaceae/butyrate/retinoic acid axis. Bioeng Transl Med 6:e10219. doi: 10.1002/btm2.10219. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B60] 60.Morais-Silva FO, Rezende AM, Pimentel C, Santos CI, Clemente C, Varela-Raposo A, Resende DM, da Silva SM, de Oliveira LM, Matos M, Costa DA, Flores O, Ruiz JC, Rodrigues-Pousada C. 2014. Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus. Microbiologyopen 3:513–530. doi: 10.1002/mbo3.184. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B61] 61.Zhang WW, Gritsenko MA, Moore RJ, Culley DE, Nie L, Petritis K, Strittmatter EF, Camp DG, Smith RD, Brockman FJ. 2006. A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry. Proteomics 6:4286–4299. doi: 10.1002/pmic.200500930. [DOI] [PubMed] [Google Scholar]

[B62] 62.Pereira PM, He Q, Valente FMA, Xavier AV, Zhou JZ, Pereira IAC, Louro RO. 2008. Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis. Antonie Van Leeuwenhoek 93:347–362. doi: 10.1007/s10482-007-9212-0. [DOI] [PubMed] [Google Scholar]

[B63] 63.Coutinho CMLM, Coutinho-Silva R, Zinkevich V, Pearce CB, Ojcius DM, Beech I. 2017. Sulphate-reducing bacteria from ulcerative colitis patients induce apoptosis of gastrointestinal epithelial cells. Microb Pathog 112:126–134. doi: 10.1016/j.micpath.2017.09.054. [DOI] [PubMed] [Google Scholar]

[B64] 64.Rowan F, Docherty NG, Murphy M, Murphy B, Calvin Coffey J, O’Connell PR. 2010. Desulfovibrio bacterial species are increased in ulcerative colitis. Dis Colon Rectum 53:1530–1536. doi: 10.1007/DCR.0b013e3181f1e620. [DOI] [PubMed] [Google Scholar]

[B65] 65.Loubinoux J, Bronowicki J-P, Pereira IAC, Mougenel J-L, Faou AE. 2002. Sulfate-reducing bacteria in human feces and their association with inflammatory bowel diseases. FEMS Microbiol Ecol 40:107–112. doi: 10.1111/j.1574-6941.2002.tb00942.x. [DOI] [PubMed] [Google Scholar]

[B66] 66.Oh JK, Chae JP, Pajarillo EAB, Kim SH, Kwak M-J, Eun J-S, Chee SW, Whang K-Y, Kim S-H, Kang D-K. 2020. Association between the body weight of growing pigs and the functional capacity of their gut microbiota. Anim Sci J 91:e13418. doi: 10.1111/asj.13418. [DOI] [PubMed] [Google Scholar]

[B67] 67.Huang J, Huang J, Li Y, Wang Y, Wang F, Qiu X, Liu X, Li H. 2021. Sodium alginate modulates immunity, intestinal mucosal barrier function, and gut microbiota in cyclophosphamide-induced immunosuppressed BALB/c mice. J Agric Food Chem 69:7064–7073. doi: 10.1021/acs.jafc.1c02294. [DOI] [PubMed] [Google Scholar]

[B68] 68.Wu S, Zuo J, Cheng Y, Zhang Y, Zhang Z, Wu M, Yang Y, Tong H. 2021. Ethanol extract of Sargarsum fusiforme alleviates HFD/STZ-induced hyperglycemia in association with modulation of gut microbiota and intestinal metabolites in type 2 diabetic mice. Food Res Int 147:110550. doi: 10.1016/j.foodres.2021.110550. [DOI] [PubMed] [Google Scholar]

[B69] 69.Pontifex MG, Mushtaq A, Le Gall G, Rodriguez-Ramiro I, Blokker BA, Hoogteijling MEM, Ricci M, Pellizzon M, Vauzour D, Müller M. 2021. Differential influence of soluble dietary fibres on intestinal and hepatic carbohydrate response. Nutrients 13:4278. doi: 10.3390/nu13124278. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B70] 70.Xing Z, Li H, Li M, Gao R, Guo C, Mi S. 2021. Disequilibrium in chicken gut microflora with avian colibacillosis is related to microenvironment damaged by antibiotics. Sci Total Environ 762:143058. doi: 10.1016/j.scitotenv.2020.143058. [DOI] [PubMed] [Google Scholar]

[B71] 71.Forbes JD, Chen C-Y, Knox NC, Marrie R-A, El-Gabalawy H, de Kievit T, Alfa M, Bernstein CN, Van Domselaar G. 2018. A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist? Microbiome 6:221. doi: 10.1186/s40168-018-0603-4. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B72] 72.Leung H, Arrazola A, Torrey S, Kiarie E. 2018. Utilization of soy hulls, oat hulls, and flax meal fiber in adult broiler breeder hens. Poult Sci 97:1368–1372. doi: 10.3382/ps/pex434. [DOI] [PubMed] [Google Scholar]

[B73] 73.Kheravii SK, Swick RA, Choct M, Wu S-B. 2018. Effect of oat hulls as a free choice feeding on broiler performance, short chain fatty acids and microflora under a mild necrotic enteritis challenge. Anim Nutr 4:65–72. doi: 10.1016/j.aninu.2017.11.003. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B74] 74.Chuang WY, Lin LJ, Shih HD, Shy YM, Chang SC, Lee TT. 2021. Intestinal microbiota, anti-inflammatory, and anti-oxidative status of broiler chickens fed diets containing mushroom waste compost by-products. Animals (Basel) 11:2550. doi: 10.3390/ani11092550. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B75] 75.Wen C, Yan W, Mai C, Duan Z, Zheng J, Sun C, Yang N. 2021. Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens. Microbiome 9:126. doi: 10.1186/s40168-021-01040-x. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B76] 76.Wen C, Yan W, Sun C, Ji C, Zhou Q, Zhang D, Zheng J, Yang N. 2019. The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens. ISME J 13:1422–1436. doi: 10.1038/s41396-019-0367-2. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B77] 77.Aragón-Vela J, Solis-Urra P, Ruiz-Ojeda FJ, Álvarez-Mercado AI, Olivares-Arancibia J, Plaza-Diaz J. 2021. Impact of exercise on gut microbiota in obesity. Nutrients 13:3999. doi: 10.3390/nu13113999. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B78] 78.Terrapon N, Henrissat B. 2014. How do gut microbes break down dietary fiber? Trends Biochem Sci 39:156–158. doi: 10.1016/j.tibs.2014.02.005. [DOI] [PubMed] [Google Scholar]

[B79] 79.Coyte KZ, Schluter J, Foster KR. 2015. The ecology of the microbiome: networks, competition, and stability. Science 350:663–666. doi: 10.1126/science.aad2602. [DOI] [PubMed] [Google Scholar]

[B80] 80.Walugembe M, Hsieh JCF, Koszewski NJ, Lamont SJ, Persia ME, Rothschild MF. 2015. Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of broiler and laying-hen chicks. Poult Sci 94:2351–2359. doi: 10.3382/ps/pev242. [DOI] [PubMed] [Google Scholar]

[B81] 81.Cui X, Gou Z, Jiang Z, Li L, Lin X, Fan Q, Wang Y, Jiang S. 2022. Dietary fiber modulates abdominal fat deposition associated with cecal microbiota and metabolites in yellow chickens. Poult Sci 101:101721. doi: 10.1016/j.psj.2022.101721. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B82] 82.Sivaprakasam S, Prasad PD, Singh N. 2016. Benefits of short-chain fatty acids and their receptors in inflammation and carcinogenesis. Pharmacol Ther 164:144–151. doi: 10.1016/j.pharmthera.2016.04.007. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B83] 83.Röhe I, Vahjen W, Metzger F, Zentek J. 2020. Effect of a “diluted” diet containing 10% lignocellulose on the gastrointestinal tract, intestinal microbiota, and excreta characteristics of dual purpose laying hens. Poult Sci 99:310–319. doi: 10.3382/ps/pez492. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B84] 84.Tomova A, Bukovsky I, Rembert E, Yonas W, Alwarith J, Barnard ND, Kahleova H. 2019. The effects of vegetarian and vegan diets on gut microbiota. Front Nutr 6:47. doi: 10.3389/fnut.2019.00047. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B85] 85.Wu W, Sun M, Chen F, Cao AT, Liu H, Zhao Y, Huang X, Xiao Y, Yao S, Zhao Q, Liu Z, Cong Y. 2017. Microbiota metabolite short-chain fatty acid acetate promotes intestinal IgA response to microbiota which is mediated by GPR43. Mucosal Immunol 10:946–956. doi: 10.1038/mi.2016.114. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B86] 86.Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, Blanchard C, Junt T, Nicod LP, Harris NL, Marsland BJ. 2014. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 20:159–166. doi: 10.1038/nm.3444. [DOI] [PubMed] [Google Scholar]

[B87] 87.Haghikia A, Jörg S, Duscha A, Berg J, Manzel A, Waschbisch A, Hammer A, Lee D-H, May C, Wilck N, Balogh A, Ostermann AI, Schebb NH, Akkad DA, Grohme DA, Kleinewietfeld M, Kempa S, Thöne J, Demir S, Müller DN, Gold R, Linker RA. 2016. Dietary fatty acids directly impact central nervous system autoimmunity via the small intestine. Immunity 44:951–953. doi: 10.1016/j.immuni.2016.04.006. [DOI] [PubMed] [Google Scholar]

[B88] 88.James KR, Gomes T, Elmentaite R, Kumar N, Gulliver EL, King HW, Stares MD, Bareham BR, Ferdinand JR, Petrova VN, Polański K, Forster SC, Jarvis LB, Suchanek O, Howlett S, James LK, Jones JL, Meyer KB, Clatworthy MR, Saeb-Parsy K, Lawley TD, Teichmann SA. 2020. Distinct microbial and immune niches of the human colon. Nat Immunol 21:343–353. doi: 10.1038/s41590-020-0602-z. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B89] 89.Lin WC, Lee TT. 2020. Laetiporus sulphureus-fermented wheat bran enhanced the broiler growth performance by improving the intestinal microflora and inflammation status. Poult Sci 99:3606–3616. doi: 10.1016/j.psj.2020.04.011. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B90] 90.Yang Y, Palm NW. 2020. Immunoglobulin A and the microbiome. Curr Opin Microbiol 56:89–96. doi: 10.1016/j.mib.2020.08.003. [DOI] [PubMed] [Google Scholar]

[B91] 91.Min YN, Yang HL, Xu YX, Gao YP. 2016. Effects of dietary supplementation of synbiotics on growth performance, intestinal morphology, sIgA content and antioxidant capacities of broilers. J Anim Physiol Anim Nutr (Berl) 100:1073–1080. doi: 10.1111/jpn.12479. [DOI] [PubMed] [Google Scholar]

[B92] 92.Shang Q, Liu H, Wu D, Mahfuz S, Piao X. 2021. Source of fiber influences growth, immune responses, gut barrier function and microbiota in weaned piglets fed antibiotic-free diets. Anim Nutr 7:315–325. doi: 10.1016/j.aninu.2020.12.008. [DOI] [PMC free article] [PubMed] [Google Scholar]

[B93] 93.Ding XM, Li DD, Bai SP, Wang JP, Zeng QF, Su ZW, Xuan Y, Zhang KY. 2018. Effect of dietary xylooligosaccharides on intestinal characteristics, gut microbiota, cecal short-chain fatty acids, and plasma immune parameters of laying hens. Poult Sci 97:874–881. doi: 10.3382/ps/pex372. [DOI] [PubMed] [Google Scholar]

PERMALINK

Longitudinal Study of the Effects of Flammulina velutipes Stipe Wastes on the Cecal Microbiota of Laying Hens

Jiali Wei

Huanwei Xiao

Yingbo Wei

Ivan Stève Nguepi Tsopmejio

Chang Sun

Haoyuan Wu

Zhouyu Jin

Hui Song

Roles

ABSTRACT

INTRODUCTION

RESULTS

The diversity of the cecal microbiota in laying hens evolves with age and diet.

FIG 1.

FIG 2.

FIG 3.

Succession of dominant gut microbiotas in the cecum of laying hens.

FIG 4.

FIG 5.

FVW supplementation altered the co-occurrence network of the cecal microbiota.

FIG 6.

FVW supplementation increased SCFA concentrations in the early life of laying hens.

TABLE 1.

FVW regulated the homeostasis of intestinal mucosal immunity in laying hens.

DISCUSSION

MATERIALS AND METHODS

Experimental design and sample collection.

TABLE 2.

DNA extraction.

PCR-DGGE and clonal sequencing.

16S rRNA high-throughput sequencing.

Determination of SCFAs concentration.

Determination of cytokines in intestinal mucosa.

Data analyses.

Ethical approval.

Data availability.

Supplementary Material

ACKNOWLEDGMENTS

Contributor Information

REFERENCES

Associated Data

Supplementary Materials

Data Availability Statement

ACTIONS

PERMALINK

RESOURCES

Similar articles

Cited by other articles

Links to NCBI Databases