This past week, Whole Foods Market (NASDAQ:WFM) disappointed shareholders with earnings that fell below lofty expectations. In recent quarters, natural and organic publicly traded competitors like Sprouts Farmers Market (NASDAQ:SFM) and The Fresh Market (NASDAQ: TFM) have slowly added to their store counts, while Kroger (NYSE:KR) continues to expand its own natural and organic offerings in its own stores.

It is estimated that the U.S. organic food market will grow at a compound annual growth rate of 14% over the next few years. Combined, sales of natural and organic foods nationwide are nearly $100 billion. Despite these trends, Whole Foods Market may have a big problem going forward.

By LoneStarMike, via Wikimedia Commons

Recent earnings for Whole Foods Market
First-quarter 2014 earnings for Whole Foods Market saw the company's total sales rise by 10% to a record $4.6 billion. However, the company's comp-sales growth of 5.4% was one of the catalysts that sent the stock tumbling nearly 8%.

The other catalyst was the lowered outlook issued by the company, which predicted full-year sales growth of 11-12% (down from 11-13%) and comp-sales growth of 5.5-6.2%. For a company that has been surpassing 7% comp-sales growth in previous years, this past week's earnings report had the market wondering whether the growth is slowing down.

Potential problems in the Whole Foods Market growth story
During the conference call, Whole Foods Market said it expected to increase its current count of 373 stores across 40 states to at least 500 stores by 2017. Long-term, the company sees a U.S. market opportunity for 1,200 locations.

However, this introduces another problem for the company, self-cannibalization.  Whole Foods has over 70 locations in California and nearly 30 in Massachusetts, while it has fewer than 10 stores in many states.

Store distribution may be one of the reasons for this comp-sales performance. It is difficult to tell whether competitors or the company's own stores are hurting its comp-sales growth. The fact that comp-sales growth for stores open for less than two years was 19.5% may just show that customers prefer to shop at newer Whole Foods Market locations.

Not only does Whole Foods Market need to pay attention to Sprouts Farmers Market and The Fresh Market, which saw their sales increase by 24% and 13% in their most recent quarters, respectively, it must also watch mainstream supermarket chains like Kroger.

Kroger's 2,414 supermarket locations across 31 states pose a serious threat to the long-term growth potential of Whole Foods Market. The Simple Truth natural and organic in-house brand is a big advantage for the supermarket giant. In Kroger's most recent earnings conference call, CEO W. Rodney McMullen commented that because of the company's large size, it can offer lower prices on organic and natural foods.

Kroger's natural and organic in-house brand Simple Truth. Credit:

Furthermore, Kroger stated that even though its natural and organic department is only its sixth- or seventh-largest department overall, it is the fastest-growing on a percentage basis by dollar amount. Kroger also has plans to add more aisle space for the department in the near future.

Competition from unlikely sources
Customers have more reasons than ever to not locate their nearest Whole Foods Market. Annie's, the natural and organic provider of pastas, meals, pizzas, dressing, and snacks at over 26,500 retail locations in the U.S. and Canada, is found in not just Whole Foods Market but in many mainstream chains around the country.

United Natural Foods is the largest distributor of natural and organic products in the U.S. and Canada. It is also the single largest third-party supplier for Whole Foods Market, where it accounts for 32% of the grocer's total purchases. However, unlike the advantage Kroger has with its Simple Truth in-house brand, Whole Foods doesn't have exclusive use of United Natural Foods.

United Natural Foods continues to add customers regularly and it now serves companies like Safeway, Costco, and even Kroger.

Competition is also coming in the form of local, regional, and international supermarkets, natural food stores, farmers' markets, and even online retailers. Restaurants also pose a threat as more of them become transparent about the exact ingredients in their menu items, with some sections of their menus specifically aimed at natural and organic diners.

Sprouts Farmers Market. Credit: Company website.

Foolish bottom line
Whole Foods Market is the victim of an increasingly competitive natural and organic environment. As a result, customers are finding alternatives at their local neighborhood markets and mainstream supermarkets that are expanding their own natural and organic selections.

Moreover, in today's world where saving time is a priority, it may make sense for customers to do all their grocery shopping at a single location that offers a wide selection of foods that includes natural and organic foods. In the end, growth beyond its main core of followers may prove difficult for Whole Foods Market -- especially if other pure natural and organic chains also continue expanding.

This article represents the opinion of the writer, who may disagree with the “official” recommendation position of a Motley Fool premium advisory service. We’re motley! Questioning an investing thesis -- even one of our own -- helps us all think critically about investing and make decisions that help us become smarter, happier, and richer.